[1] "ofn"       "-oTLGG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/15082624/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15716584/transformed.cor.cli.txt"

nPatients in clinical file=475, in cluster file=513, common to both=473
[1] "Reduce the number of clustering variables from 148 to 143."
[1] 143 473
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           367            106 
  IDH1 MUTATED IDH1 WILD-TYPE 
           367            106 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           226            247 
  TP53 MUTATED TP53 WILD-TYPE 
           226            247 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
           181            292 
  ATRX MUTATED ATRX WILD-TYPE 
           181            292 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
          100           373 
  CIC MUTATED CIC WILD-TYPE 
          100           373 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              42              431 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              42              431 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            30            443 
  EGFR MUTATED EGFR WILD-TYPE 
            30            443 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              20              453 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              20              453 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            19            454 
  IDH2 MUTATED IDH2 WILD-TYPE 
            19            454 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           31           442 
  NF1 MUTATED NF1 WILD-TYPE 
           31           442 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            23            450 
  PTEN MUTATED PTEN WILD-TYPE 
            23            450 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             46             427 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             46             427 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              454 
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              454 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              42              431 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              42              431 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
             10             463 
  STK19 MUTATED STK19 WILD-TYPE 
             10             463 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
             17             456 
  NIPBL MUTATED NIPBL WILD-TYPE 
             17             456 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               6              467 
  CREBZF MUTATED CREBZF WILD-TYPE 
               6              467 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
             15             458 
  TCF12 MUTATED TCF12 WILD-TYPE 
             15             458 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               6              467 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               6              467 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             3            470 
  SRPX MUTATED SRPX WILD-TYPE 
             3            470 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               24               449 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               24               449 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            466 
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            466 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
              18              455 
  FAM47C MUTATED FAM47C WILD-TYPE 
              18              455 
[1] "TNRC18 MUTATION ANALYSIS"
[1] 3
  TNRC18 MUTATED TNRC18 WILD-TYPE 
              10              463 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
              10              463 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              463 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              463 
[1] "HTRA2 MUTATION ANALYSIS"
[1] 3
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              5             468 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              5             468 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              469 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              469 
[1] "RBPJ MUTATION ANALYSIS"
[1] 3
  RBPJ MUTATED RBPJ WILD-TYPE 
             7            466 
  RBPJ MUTATED RBPJ WILD-TYPE 
             7            466 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             4            469 
  NRAS MUTATED NRAS WILD-TYPE 
             4            469 
[1] "ZNF292 MUTATION ANALYSIS"
[1] 3
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              13              460 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              13              460 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              466 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              466 
[1] "GAGE2D MUTATION ANALYSIS"
[1] 3
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              468 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              468 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             11             462 
  ARID2 MUTATED ARID2 WILD-TYPE 
             11             462 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              8             465 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              8             465 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               8              465 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               8              465 
[1] "ZNF512B MUTATION ANALYSIS"
[1] 3
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                4               469 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                4               469 
[1] "PPL MUTATION ANALYSIS"
[1] 3
  PPL MUTATED PPL WILD-TYPE 
            5           468 
  PPL MUTATED PPL WILD-TYPE 
            5           468 
[1] "PRX MUTATION ANALYSIS"
[1] 3
  PRX MUTATED PRX WILD-TYPE 
           10           463 
  PRX MUTATED PRX WILD-TYPE 
           10           463 
[1] "NKD2 MUTATION ANALYSIS"
[1] 3
  NKD2 MUTATED NKD2 WILD-TYPE 
             4            469 
  NKD2 MUTATED NKD2 WILD-TYPE 
             4            469 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
             7            466 
  IRS4 MUTATED IRS4 WILD-TYPE 
             7            466 
[1] "SPTAN1 MUTATION ANALYSIS"
[1] 3
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               5              468 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               5              468 
[1] "CIB1 MUTATION ANALYSIS"
[1] 3
  CIB1 MUTATED CIB1 WILD-TYPE 
             4            469 
  CIB1 MUTATED CIB1 WILD-TYPE 
             4            469 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              469 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              469 
[1] "SCN4A MUTATION ANALYSIS"
[1] 3
  SCN4A MUTATED SCN4A WILD-TYPE 
              6             467 
  SCN4A MUTATED SCN4A WILD-TYPE 
              6             467 
[1] "PLCG1 MUTATION ANALYSIS"
[1] 3
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              6             467 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              6             467 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             5            468 
  DLC1 MUTATED DLC1 WILD-TYPE 
             5            468 
[1] "TMEM216 MUTATION ANALYSIS"
[1] 3
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               470 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               470 
[1] "MYT1 MUTATION ANALYSIS"
[1] 3
  MYT1 MUTATED MYT1 WILD-TYPE 
             6            467 
  MYT1 MUTATED MYT1 WILD-TYPE 
             6            467 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               469 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               469 
[1] "RIPK4 MUTATION ANALYSIS"
[1] 3
  RIPK4 MUTATED RIPK4 WILD-TYPE 
              8             465 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
              8             465 
[1] "NEU2 MUTATION ANALYSIS"
[1] 3
  NEU2 MUTATED NEU2 WILD-TYPE 
             4            469 
  NEU2 MUTATED NEU2 WILD-TYPE 
             4            469 
[1] "PTPRH MUTATION ANALYSIS"
[1] 3
  PTPRH MUTATED PTPRH WILD-TYPE 
              8             465 
  PTPRH MUTATED PTPRH WILD-TYPE 
              8             465 
[1] "MAPK15 MUTATION ANALYSIS"
[1] 3
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               4              469 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               4              469 
[1] "TPX2 MUTATION ANALYSIS"
[1] 3
  TPX2 MUTATED TPX2 WILD-TYPE 
             3            470 
  TPX2 MUTATED TPX2 WILD-TYPE 
             3            470 
[1] "SLC12A7 MUTATION ANALYSIS"
[1] 3
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                5               468 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                5               468 
[1] "PLXNA3 MUTATION ANALYSIS"
[1] 3
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               8              465 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               8              465 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           467 
  RET MUTATED RET WILD-TYPE 
            6           467 
[1] "ZNF148 MUTATION ANALYSIS"
[1] 3
  ZNF148 MUTATED ZNF148 WILD-TYPE 
               4              469 
  ZNF148 MUTATED ZNF148 WILD-TYPE 
               4              469 
[1] "HDAC2 MUTATION ANALYSIS"
[1] 3
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              4             469 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              4             469 
[1] "RBBP6 MUTATION ANALYSIS"
[1] 3
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              6             467 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              6             467 
[1] "MED9 MUTATION ANALYSIS"
[1] 3
  MED9 MUTATED MED9 WILD-TYPE 
             3            470 
  MED9 MUTATED MED9 WILD-TYPE 
             3            470 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             5            468 
  DDX5 MUTATED DDX5 WILD-TYPE 
             5            468 
[1] "ZC3H11A MUTATION ANALYSIS"
[1] 3
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               468 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               468 
[1] "SLC6A3 MUTATION ANALYSIS"
[1] 3
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               9              464 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               9              464 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              5             468 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              5             468 
[1] "C4BPA MUTATION ANALYSIS"
[1] 3
  C4BPA MUTATED C4BPA WILD-TYPE 
              4             469 
  C4BPA MUTATED C4BPA WILD-TYPE 
              4             469 
[1] "MATK MUTATION ANALYSIS"
[1] 3
  MATK MUTATED MATK WILD-TYPE 
             5            468 
  MATK MUTATED MATK WILD-TYPE 
             5            468 
[1] "SMOC1 MUTATION ANALYSIS"
[1] 3
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              3             470 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              3             470 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               4              469 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               4              469 
[1] "CD99L2 MUTATION ANALYSIS"
[1] 3
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               3              470 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               3              470 
[1] "SELE MUTATION ANALYSIS"
[1] 3
  SELE MUTATED SELE WILD-TYPE 
             6            467 
  SELE MUTATED SELE WILD-TYPE 
             6            467 
[1] "TMEM184A MUTATION ANALYSIS"
[1] 3
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 3                470 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 3                470 
[1] "FHOD1 MUTATION ANALYSIS"
[1] 3
  FHOD1 MUTATED FHOD1 WILD-TYPE 
              6             467 
  FHOD1 MUTATED FHOD1 WILD-TYPE 
              6             467 
[1] "HTR3A MUTATION ANALYSIS"
[1] 3
  HTR3A MUTATED HTR3A WILD-TYPE 
              7             466 
  HTR3A MUTATED HTR3A WILD-TYPE 
              7             466 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            5           468 
  RB1 MUTATED RB1 WILD-TYPE 
            5           468 
[1] "FGD6 MUTATION ANALYSIS"
[1] 3
  FGD6 MUTATED FGD6 WILD-TYPE 
             4            469 
  FGD6 MUTATED FGD6 WILD-TYPE 
             4            469 
[1] "CD72 MUTATION ANALYSIS"
[1] 3
  CD72 MUTATED CD72 WILD-TYPE 
             3            470 
  CD72 MUTATED CD72 WILD-TYPE 
             3            470 
[1] "NKPD1 MUTATION ANALYSIS"
[1] 3
  NKPD1 MUTATED NKPD1 WILD-TYPE 
              3             470 
  NKPD1 MUTATED NKPD1 WILD-TYPE 
              3             470 
[1] "MTMR1 MUTATION ANALYSIS"
[1] 3
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              4             469 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              4             469 
[1] "GPR133 MUTATION ANALYSIS"
[1] 3
  GPR133 MUTATED GPR133 WILD-TYPE 
               3              470 
  GPR133 MUTATED GPR133 WILD-TYPE 
               3              470 
[1] "CNOT4 MUTATION ANALYSIS"
[1] 3
  CNOT4 MUTATED CNOT4 WILD-TYPE 
              5             468 
  CNOT4 MUTATED CNOT4 WILD-TYPE 
              5             468 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              19              454 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              19              454 
[1] "ROBO3 MUTATION ANALYSIS"
[1] 3
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             469 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             469 
[1] "PDE8A MUTATION ANALYSIS"
[1] 3
  PDE8A MUTATED PDE8A WILD-TYPE 
              6             467 
  PDE8A MUTATED PDE8A WILD-TYPE 
              6             467 
[1] "EEF1D MUTATION ANALYSIS"
[1] 3
  EEF1D MUTATED EEF1D WILD-TYPE 
              3             470 
  EEF1D MUTATED EEF1D WILD-TYPE 
              3             470 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
            7           466 
  MET MUTATED MET WILD-TYPE 
            7           466 
[1] "CUL4B MUTATION ANALYSIS"
[1] 3
  CUL4B MUTATED CUL4B WILD-TYPE 
             10             463 
  CUL4B MUTATED CUL4B WILD-TYPE 
             10             463 
[1] "SNX31 MUTATION ANALYSIS"
[1] 3
  SNX31 MUTATED SNX31 WILD-TYPE 
              4             469 
  SNX31 MUTATED SNX31 WILD-TYPE 
              4             469 
[1] "PHF3 MUTATION ANALYSIS"
[1] 3
  PHF3 MUTATED PHF3 WILD-TYPE 
             8            465 
  PHF3 MUTATED PHF3 WILD-TYPE 
             8            465 
[1] "G6PC MUTATION ANALYSIS"
[1] 3
  G6PC MUTATED G6PC WILD-TYPE 
             5            468 
  G6PC MUTATED G6PC WILD-TYPE 
             5            468 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             470 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             470 
[1] "AEBP1 MUTATION ANALYSIS"
[1] 3
  AEBP1 MUTATED AEBP1 WILD-TYPE 
              4             469 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
              4             469 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
              8             465 
  SETD2 MUTATED SETD2 WILD-TYPE 
              8             465 
[1] "DST MUTATION ANALYSIS"
[1] 3
  DST MUTATED DST WILD-TYPE 
           11           462 
  DST MUTATED DST WILD-TYPE 
           11           462 
[1] "USP6 MUTATION ANALYSIS"
[1] 3
  USP6 MUTATED USP6 WILD-TYPE 
             5            468 
  USP6 MUTATED USP6 WILD-TYPE 
             5            468 
[1] "TPM1 MUTATION ANALYSIS"
[1] 3
  TPM1 MUTATED TPM1 WILD-TYPE 
             5            468 
  TPM1 MUTATED TPM1 WILD-TYPE 
             5            468 
[1] "GLYAT MUTATION ANALYSIS"
[1] 3
  GLYAT MUTATED GLYAT WILD-TYPE 
              4             469 
  GLYAT MUTATED GLYAT WILD-TYPE 
              4             469 
[1] "DIAPH1 MUTATION ANALYSIS"
[1] 3
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               4              469 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               4              469 
[1] "ZMYM2 MUTATION ANALYSIS"
[1] 3
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              6             467 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              6             467 
[1] "HCFC1 MUTATION ANALYSIS"
[1] 3
  HCFC1 MUTATED HCFC1 WILD-TYPE 
              7             466 
  HCFC1 MUTATED HCFC1 WILD-TYPE 
              7             466 
[1] "MST1 MUTATION ANALYSIS"
[1] 3
  MST1 MUTATED MST1 WILD-TYPE 
             4            469 
  MST1 MUTATED MST1 WILD-TYPE 
             4            469 
[1] "TNFSF14 MUTATION ANALYSIS"
[1] 3
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
                5               468 
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
                5               468 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             10             463 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             10             463 
[1] "ENGASE MUTATION ANALYSIS"
[1] 3
  ENGASE MUTATED ENGASE WILD-TYPE 
               3              470 
  ENGASE MUTATED ENGASE WILD-TYPE 
               3              470 
[1] "MYH8 MUTATION ANALYSIS"
[1] 3
  MYH8 MUTATED MYH8 WILD-TYPE 
            11            462 
  MYH8 MUTATED MYH8 WILD-TYPE 
            11            462 
[1] "VSIG4 MUTATION ANALYSIS"
[1] 3
  VSIG4 MUTATED VSIG4 WILD-TYPE 
              6             467 
  VSIG4 MUTATED VSIG4 WILD-TYPE 
              6             467 
[1] "KRT3 MUTATION ANALYSIS"
[1] 3
  KRT3 MUTATED KRT3 WILD-TYPE 
             4            469 
  KRT3 MUTATED KRT3 WILD-TYPE 
             4            469 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
              4             469 
  STAG2 MUTATED STAG2 WILD-TYPE 
              4             469 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             24             449 
  MUC17 MUTATED MUC17 WILD-TYPE 
             24             449 
[1] "ABCA7 MUTATION ANALYSIS"
[1] 3
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              9             464 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              9             464 
[1] "FOXK1 MUTATION ANALYSIS"
[1] 3
  FOXK1 MUTATED FOXK1 WILD-TYPE 
              4             469 
  FOXK1 MUTATED FOXK1 WILD-TYPE 
              4             469 
[1] "SLFN11 MUTATION ANALYSIS"
[1] 3
  SLFN11 MUTATED SLFN11 WILD-TYPE 
               3              470 
  SLFN11 MUTATED SLFN11 WILD-TYPE 
               3              470 
[1] "MX2 MUTATION ANALYSIS"
[1] 3
  MX2 MUTATED MX2 WILD-TYPE 
            4           469 
  MX2 MUTATED MX2 WILD-TYPE 
            4           469 
[1] "SLC6A4 MUTATION ANALYSIS"
[1] 3
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
               4              469 
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
               4              469 
[1] "KRT15 MUTATION ANALYSIS"
[1] 3
  KRT15 MUTATED KRT15 WILD-TYPE 
              6             467 
  KRT15 MUTATED KRT15 WILD-TYPE 
              6             467 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
           8          465 
  F8 MUTATED F8 WILD-TYPE 
           8          465 
[1] "HOOK1 MUTATION ANALYSIS"
[1] 3
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              3             470 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              3             470 
[1] "FMR1 MUTATION ANALYSIS"
[1] 3
  FMR1 MUTATED FMR1 WILD-TYPE 
             5            468 
  FMR1 MUTATED FMR1 WILD-TYPE 
             5            468 
[1] "SON MUTATION ANALYSIS"
[1] 3
  SON MUTATED SON WILD-TYPE 
            8           465 
  SON MUTATED SON WILD-TYPE 
            8           465 
[1] "TTC30B MUTATION ANALYSIS"
[1] 3
  TTC30B MUTATED TTC30B WILD-TYPE 
               6              467 
  TTC30B MUTATED TTC30B WILD-TYPE 
               6              467 
[1] "FANCD2 MUTATION ANALYSIS"
[1] 3
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              466 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              466 
[1] "RGL2 MUTATION ANALYSIS"
[1] 3
  RGL2 MUTATED RGL2 WILD-TYPE 
             4            469 
  RGL2 MUTATED RGL2 WILD-TYPE 
             4            469 
[1] "NR1H3 MUTATION ANALYSIS"
[1] 3
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              4             469 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              4             469 
[1] "TYRP1 MUTATION ANALYSIS"
[1] 3
  TYRP1 MUTATED TYRP1 WILD-TYPE 
              4             469 
  TYRP1 MUTATED TYRP1 WILD-TYPE 
              4             469 
[1] "SLC25A5 MUTATION ANALYSIS"
[1] 3
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
                4               469 
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
                4               469 
[1] "AGBL1 MUTATION ANALYSIS"
[1] 3
  AGBL1 MUTATED AGBL1 WILD-TYPE 
              4             469 
  AGBL1 MUTATED AGBL1 WILD-TYPE 
              4             469 
[1] "AMPD1 MUTATION ANALYSIS"
[1] 3
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              4             469 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              4             469 
[1] "NGEF MUTATION ANALYSIS"
[1] 3
  NGEF MUTATED NGEF WILD-TYPE 
             5            468 
  NGEF MUTATED NGEF WILD-TYPE 
             5            468 
[1] "YIPF1 MUTATION ANALYSIS"
[1] 3
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             470 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             470 
[1] "PDHA1 MUTATION ANALYSIS"
[1] 3
  PDHA1 MUTATED PDHA1 WILD-TYPE 
              5             468 
  PDHA1 MUTATED PDHA1 WILD-TYPE 
              5             468 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              3             470 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              3             470 
[1] "HLA-DRA MUTATION ANALYSIS"
[1] 3
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                3               470 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                3               470 
[1] "ALPP MUTATION ANALYSIS"
[1] 3
  ALPP MUTATED ALPP WILD-TYPE 
             4            469 
  ALPP MUTATED ALPP WILD-TYPE 
             4            469 
[1] "CDH3 MUTATION ANALYSIS"
[1] 3
  CDH3 MUTATED CDH3 WILD-TYPE 
             3            470 
  CDH3 MUTATED CDH3 WILD-TYPE 
             3            470 
[1] "NADSYN1 MUTATION ANALYSIS"
[1] 3
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
                3               470 
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
                3               470 
[1] "LHFPL1 MUTATION ANALYSIS"
[1] 3
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
               4              469 
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
               4              469 
[1] "CXCR2 MUTATION ANALYSIS"
[1] 3
  CXCR2 MUTATED CXCR2 WILD-TYPE 
              4             469 
  CXCR2 MUTATED CXCR2 WILD-TYPE 
              4             469 
[1] "SEC14L4 MUTATION ANALYSIS"
[1] 3
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
                3               470 
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
                3               470 
[1] "ANKRD17 MUTATION ANALYSIS"
[1] 3
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                6               467 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                6               467 
[1] "MAST3 MUTATION ANALYSIS"
[1] 3
  MAST3 MUTATED MAST3 WILD-TYPE 
              5             468 
  MAST3 MUTATED MAST3 WILD-TYPE 
              5             468 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               470 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               470 
[1] "NEO1 MUTATION ANALYSIS"
[1] 3
  NEO1 MUTATED NEO1 WILD-TYPE 
             7            466 
  NEO1 MUTATED NEO1 WILD-TYPE 
             7            466 
[1] "IGSF8 MUTATION ANALYSIS"
[1] 3
  IGSF8 MUTATED IGSF8 WILD-TYPE 
              3             470 
  IGSF8 MUTATED IGSF8 WILD-TYPE 
              3             470 
[1] "RGS3 MUTATION ANALYSIS"
[1] 3
  RGS3 MUTATED RGS3 WILD-TYPE 
             5            468 
  RGS3 MUTATED RGS3 WILD-TYPE 
             5            468 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"              
[10] "RADIATION_THERAPY"                     
[11] "KARNOFSKY_PERFORMANCE_SCORE"           
[12] "HISTOLOGICAL_TYPE"                     
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 473 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=91,	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=355,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 10:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 473 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = IDH1 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED   312  53
  IDH1 WILD-TYPE  66  40
  IDH1 MUTATED IDH1 WILD-TYPE 
           365            106 
  IDH1 MUTATED IDH1 WILD-TYPE 
            53             40 
$`IDH1 MUTATED`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.95        12.43         8.48         7.56 
TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        8.02         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       33.57        31.63        24.20        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       11.24        17.88        30.74        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US 
       30.21        42.05        27.81        17.19        17.19        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 
       13.38         3.45        18.61        17.46        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6407 
       49.02        75.16        46.06         1.22        87.45        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
       14.99       105.21        90.77        30.67        26.30        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       41.98        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       14.24        12.59        15.12         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        2.70        77.98         7.23         5.98         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
       17.98       124.50        23.51        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93       134.27        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
        0.20        47.77        34.36        36.82        14.93        24.99 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       23.97        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       38.27        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        22.26        28.54        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       20.45        13.58        27.52         0.10         6.67        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 
        0.13         0.03        16.54         3.75        17.42        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7684 TCGA-HT-7686 
        0.23        14.27         0.16        16.24         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 
        0.10        31.69        14.96         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
        6.90        14.53        19.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8105 
       31.43         1.64         9.40        63.55        37.87         6.25 
TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
        0.10         2.50         5.56         0.23        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       26.04         0.13        20.22         0.10         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A74J 
        1.81        16.83        21.40         6.38        17.52        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       19.23         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       20.35        20.81        20.71        19.00        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A731 
        7.63         0.76        10.42        13.25        11.64         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CU 
       13.61        15.16         2.53        12.62        14.04        14.83 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.73         1.91        16.50        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        37.84        34.49        28.70        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
       18.61        15.16        14.07        36.13         7.92        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.12        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        11.97        48.33        49.32        34.78        48.39 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        30.44        28.08        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       33.24        25.38        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       43.04        13.51         0.10        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

$`IDH1 WILD-TYPE`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6669 
        7.69        21.01         6.38        17.69        23.84         7.40 
TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-A7UR 
       72.95        25.48        16.18        19.96        31.82        54.25 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6399 
       18.02        14.56         6.74         8.45       211.17        65.75 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 
        7.04        11.64       133.74        19.89        16.83        11.47 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7309 TCGA-DU-8158 
        6.54         8.84        10.36         7.96         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A76K 
       23.74        14.60        19.13         4.96        12.20        11.41 
TCGA-DU-A76L TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5318 
       26.76        77.88        42.31         7.50         0.56        78.21 
TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 
       25.48        18.77        18.44        20.09        12.95        22.52 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7476 
       10.72        18.38        10.78         5.72        11.54         6.54 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
        0.76        44.68         0.10        39.48        39.09         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
        0.49         3.72        16.24         0.10        33.01        12.23 
TCGA-HT-8107 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DS 
        0.46        13.78        29.59        13.74        15.72         0.23 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H 
        0.07        27.35         5.33        16.14        17.65         2.43 
TCGA-HW-7491 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-P5-A72U 
       40.18        12.76        14.40         2.37         1.28         0.16 
TCGA-P5-A730 TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC 
        0.20        15.85        19.33        14.53        12.23         5.03 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7QY 
       31.33        22.95         5.85        19.86        22.32        28.37 
TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84J 
       10.39        18.71        49.45        24.92        16.18        24.16 
TCGA-TM-A84R TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       18.61        30.08         7.89         8.05 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.03           0.07 
  IDH1 MUTATED IDH1 WILD-TYPE 
        182.33         211.17 
  IDH1 MUTATED IDH1 WILD-TYPE 
         20.09          14.58 
[1] "0.0 - 182.3 (20.1)" "0.1 - 211.2 (14.6)"
[1] "hr=" "4.3"
D1V2, continuous
D1V3, binary
                cls
clus               0   1
  IDH1 MUTATED   159 208
  IDH1 WILD-TYPE  48  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED    159  208
  IDH1 WILD-TYPE   48   58
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE          159             48
  MALE            208             58
[1] 2 2
[1] FALSE
D1V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IDH1 MUTATED           122              100               145
  IDH1 WILD-TYPE          53               19                34
D1V5, multiclass
                   clus
vv                  IDH1 MUTATED IDH1 WILD-TYPE
  ASTROCYTOMA                122             53
  OLIGOASTROCYTOMA           100             19
  OLIGODENDROGLIOMA          145             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  IDH1 MUTATED    70 297
  IDH1 WILD-TYPE  22  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     70  297
  IDH1 WILD-TYPE   22   84
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            70             22
  YES          297             84
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH1 MUTATED                                  0     6
  IDH1 WILD-TYPE                                1     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED                           9   343
  IDH1 WILD-TYPE                         6    95
D1V7, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       6              2
  BLACK OR AFRICAN AMERICAN                   9              6
  WHITE                                     343             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                cls
clus               0   1
  IDH1 MUTATED    13 327
  IDH1 WILD-TYPE   5  93
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     13  327
  IDH1 WILD-TYPE    5   93
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO               13              5
  NOT HISPANIC OR LATINO          327             93
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   185  40
  TP53 WILD-TYPE 193  53
  TP53 MUTATED TP53 WILD-TYPE 
           225            246 
  TP53 MUTATED TP53 WILD-TYPE 
            40             53 
$`TP53 MUTATED`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5396 TCGA-CS-6290 
        4.70        43.89        18.15        40.18         9.96        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
       12.43         8.48         7.56       122.73        81.96        47.93 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       50.86        36.56        78.28        46.42        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L 
       39.78        37.45        33.57        27.45        18.51        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B 
       17.88        30.74        19.96        30.31        14.40        42.05 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5851 
       27.81        17.19        13.38         3.45        18.61        17.46 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
       13.38         6.81        18.94        17.49       211.17        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
       75.16        65.75        87.45        94.52       114.08         7.73 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 
       62.96       156.23        14.99       105.21         8.84        90.77 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 
       26.30        18.94        44.02        62.01        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       41.98         2.76        20.68        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 
       14.24        12.59         4.96         3.65         5.65         7.23 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC TCGA-E1-5302 TCGA-E1-5303 
        7.13       124.50        77.88        23.51        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YW TCGA-E1-A7Z6 
       41.13        79.99        57.93       130.78        36.82        32.35 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
        0.20        25.48        36.82        14.93        24.99        23.97 
TCGA-FG-7636 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       17.88        13.68        14.24        14.96        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y 
       18.71        23.70        14.76        16.41        22.26        28.54 
TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
       48.69        27.52        11.54        40.11         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 
      122.47        17.29        45.99        56.09        57.60         0.16 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 
       42.74        31.69        14.96         0.10        17.52        19.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7884 TCGA-HT-7902 
       50.63        23.61         3.68         5.33        11.28        31.43 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8111 
       63.55        37.87         6.25         0.10         2.50         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5RB 
       34.19        28.27        15.72         0.23         0.13         0.10 
TCGA-HT-A614 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 
        2.70        16.83        17.52        10.52         0.10         8.32 
TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM 
       19.23        21.70        21.60        19.59        20.81        20.71 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
       19.00         0.23         6.71         2.30         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CW 
        0.76        10.42        13.25        13.61         2.53        13.61 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-RY-A83Z 
        9.17        10.29         1.91        16.50        12.99         9.90 
TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U6 
       19.59        62.17        87.12        18.77        28.70        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IZ 
       98.24        95.93        80.12        18.61        14.07         7.13 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 
       20.02        15.06        13.12        13.02        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       98.63        31.59        11.97        48.33        34.78        48.39 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VV-A86M 
       25.38        23.80        15.98        26.99        43.04        16.01 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

$`TP53 WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 
        7.69        10.62        64.64         0.10        21.01         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5274 
       17.69        23.84         8.02         7.40         6.61        75.25 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       72.92        50.17        44.52        18.84        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       24.20        25.48        30.12         5.98        31.40        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5144 
       29.23        14.40        12.10        16.18        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5847 TCGA-DU-5849 
       30.21        17.19        54.25        13.12        18.02        14.56 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
        6.74         8.45       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       46.06         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7012 TCGA-DU-7018 
       16.83         7.96        11.47       138.28         6.54        30.67 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 
       10.36         7.96        94.32        60.30         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A5TY TCGA-DU-A6S2 
       14.60        21.40        14.17        15.12        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
        2.70        77.98         5.98        11.41        26.76        21.30 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5311 
       17.98        42.31         7.50        44.42         0.56       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O3 
       78.21        95.57        75.02        32.45        14.33         0.23 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7637 
       47.77        34.36        18.77        18.44        15.35        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 
       22.55        20.61        20.09        12.95        16.01        20.09 
TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       22.52        10.72        18.38        17.82        15.02        16.44 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7467 
       10.78        36.66        20.45        13.58         5.72         0.10 
TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 
        6.67         0.13        75.19        95.93         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       22.06         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
        6.05         0.10         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.48        39.09         0.23         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        0.13        35.47         3.72         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 
        0.10        33.01        12.23         0.46         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       29.59        13.74        26.04        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61A 
        5.33        16.93         1.81        16.14        21.40         6.38 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 
       17.65         2.43        15.35        11.05        29.92        19.89 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-IK-8125 
       40.18         4.31        17.82        20.35        12.76        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F6 
       14.40        14.40         1.64         2.37         4.11         1.28 
TCGA-P5-A72U TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65V 
        0.16        11.64         0.20         9.01        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
       15.85        14.04        19.33        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XC TCGA-QH-A86X 
        2.20        14.53        16.34        16.73         5.03        11.08 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       28.08         2.07        30.67        37.84        34.49        31.33 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UA TCGA-S9-A6UB 
       22.95        17.62        23.64        32.61         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       69.50        72.59        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.91        15.16        36.13         7.92        22.32        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 
        8.19         2.04        17.03        28.37       169.84        10.39 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G 
       18.71        49.45        49.32        24.92        16.18        40.64 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       33.24        18.61        14.93        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
        7.89        35.93        23.47        37.05        23.21        51.06 

  TP53 MUTATED TP53 WILD-TYPE 
          0.03           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        211.17         182.33 
  TP53 MUTATED TP53 WILD-TYPE 
         20.68          16.78 
[1] "0.0 - 211.2 (20.7)" "0.1 - 182.3 (16.8)"
[1] "hr=" "1.6"
D2V2, continuous
D2V3, binary
                cls
clus               0   1
  TP53 MUTATED    92 134
  TP53 WILD-TYPE 115 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     92  134
  TP53 WILD-TYPE  115  132
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           92            115
  MALE            134            132
[1] 2 2
[1] FALSE
D2V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TP53 MUTATED           116               69                41
  TP53 WILD-TYPE          59               50               138
D2V5, multiclass
                   clus
vv                  TP53 MUTATED TP53 WILD-TYPE
  ASTROCYTOMA                116             59
  OLIGOASTROCYTOMA            69             50
  OLIGODENDROGLIOMA           41            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus               0   1
  TP53 MUTATED    56 170
  TP53 WILD-TYPE  36 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     56  170
  TP53 WILD-TYPE   36  211
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            56             36
  YES          170            211
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     1
  TP53 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           5   217
  TP53 WILD-TYPE                        10   221
D2V7, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              7
  BLACK OR AFRICAN AMERICAN                   5             10
  WHITE                                     217            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                cls
clus               0   1
  TP53 MUTATED    10 202
  TP53 WILD-TYPE   8 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     10  202
  TP53 WILD-TYPE    8  218
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO               10              8
  NOT HISPANIC OR LATINO          202            218
[1] 2 2
[1] FALSE

Clustering(3) Variable = ATRX MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  ATRX MUTATED   144  36
  ATRX WILD-TYPE 234  57
  ATRX MUTATED ATRX WILD-TYPE 
           180            291 
  ATRX MUTATED ATRX WILD-TYPE 
            36             57 
$`ATRX MUTATED`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5270 TCGA-DB-5273 
        4.70        43.89        18.15         8.48       122.73        81.96 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC 
       47.93        72.92        36.56        78.28        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64S TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 
       39.78        37.45        27.45        17.88        30.74        30.31 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UV TCGA-DU-5851 
        8.02        42.05        27.81        17.19        18.61        17.46 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
       13.38         6.81        18.94        17.49       211.17        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7007 
       75.16        65.75        87.45        94.52       114.08        62.96 
TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7015 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 
      156.23       105.21        90.77        18.94        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       41.98         2.76        20.68        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O 
       12.59        15.12         3.65         5.65         7.23         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        77.88        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 
       57.93       130.78        32.45        36.82        32.35         0.20 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
       25.48        36.82        14.93        24.99        23.97        17.88 
TCGA-FG-7638 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       22.55        13.68        14.24        14.96        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A70Y TCGA-FG-A711 TCGA-FG-A713 TCGA-FN-7833 
       18.71        23.70        28.54        48.69        20.45        27.52 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       11.54        40.11         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        6.54        24.26         6.38       106.95       172.77         4.01 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7686 
       23.18       122.47        56.09        57.60         0.16        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 
       31.69        14.96         0.10        17.52        19.23         0.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7884 TCGA-HT-7902 
       50.63        23.61         3.68         5.33        11.28        31.43 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8108 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R5 
       63.55        37.87         2.50        34.19        28.27         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74J 
       20.22         0.10         2.70         1.81        16.83        10.52 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-A5KL TCGA-HW-A5KM 
        0.10         8.32        19.23        21.70        20.81        20.71 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72W 
       19.00         0.23         6.71         5.88         7.63        10.42 
TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X8 
       13.25        13.61         2.53        13.61        10.29        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6TV 
        1.91        16.50        12.99         9.90        62.17        18.77 
TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG 
       17.62        16.08        98.24        95.93         5.85        80.12 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QX 
       18.61        14.07         7.92         7.13        15.06        13.12 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84I 
       98.63        31.59        18.71        48.33        34.78        28.08 
TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       40.83        25.38        23.80        15.98        26.99        43.04 
TCGA-VM-A8CH TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D TCGA-WY-A85E 
       23.47        43.96        43.40        45.80        37.71        20.81 

$`ATRX WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
        7.69        10.62        64.64        40.18         0.10        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        9.96         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5274 TCGA-DB-5277 
        7.56         8.02         7.40         6.61        75.25        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XF TCGA-DB-A4XG 
       50.17        44.52        46.42        18.84        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66F 
       16.18        19.96        31.82        14.40        30.21        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 
       54.25        13.12        13.38         3.45        18.02        14.56 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
        6.74         8.45       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       46.06         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 
       16.83         7.96         7.73        11.47       138.28        14.99 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54         8.84        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 
       94.32        44.02        62.01        60.30         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TY 
       14.60        21.40        19.13        14.17         4.96        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
       21.30        17.98        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-EZ-7264 
        0.56       134.27        78.21        95.57        75.02        14.33 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7634 
        0.23        47.77        34.36        18.77        18.44        15.35 
TCGA-FG-7637 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 
       40.08        20.61        20.09        12.95        16.01        20.09 
TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       22.52        10.72        18.38        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87N 
       15.02        16.44        22.26        10.78        36.66        13.58 
TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7479 TCGA-HT-7480 
        5.72         0.10         6.67         0.13        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       95.93         5.03        29.85         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 
       22.06        45.99         0.23        14.27        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
       44.68         6.05         0.10         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       14.53        39.48        39.09         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        0.13        35.47         3.72         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        0.10        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 
        5.56        13.78         0.23        29.59        13.74        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 
        0.23        26.04         0.07        27.35         5.33        16.93 
TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.14        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 
       15.35        11.05        29.92        19.89        40.18         4.31 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-IK-8125 
       21.60        19.59        17.82        20.35        12.76        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
       14.40        14.40         1.64         2.37         2.30         4.11 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.76         1.28         0.16        11.64         0.20         9.01 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.53        12.23         2.20         9.17        14.53        16.34 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        5.03        11.08        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       23.64        32.61       106.39        69.50        72.59        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ 
       84.99        31.10        19.86        15.91        15.16        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51        20.02         8.19         2.04        17.03 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       11.97        49.45        49.32        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O 
       59.05        40.64        30.44        24.16        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       18.61        14.93        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       35.93        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85C 
       13.32        39.88        46.88 

  ATRX MUTATED ATRX WILD-TYPE 
          0.03           0.07 
  ATRX MUTATED ATRX WILD-TYPE 
        211.17         182.33 
  ATRX MUTATED ATRX WILD-TYPE 
         20.81          17.03 
[1] "0.0 - 211.2 (20.8)" "0.1 - 182.3 (17.0)"
[1] "hr=" "1.4"
D3V2, continuous
D3V3, binary
                cls
clus               0   1
  ATRX MUTATED    77 104
  ATRX WILD-TYPE 130 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     77  104
  ATRX WILD-TYPE  130  162
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           77            130
  MALE            104            162
[1] 2 2
[1] FALSE
D3V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ATRX MUTATED            86               61                34
  ATRX WILD-TYPE          89               58               145
D3V5, multiclass
                   clus
vv                  ATRX MUTATED ATRX WILD-TYPE
  ASTROCYTOMA                 86             89
  OLIGOASTROCYTOMA            61             58
  OLIGODENDROGLIOMA           34            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus               0   1
  ATRX MUTATED    46 135
  ATRX WILD-TYPE  46 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     46  135
  ATRX WILD-TYPE   46  246
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            46             46
  YES          135            246
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATRX MUTATED                                  0     1
  ATRX WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATRX MUTATED                           6   173
  ATRX WILD-TYPE                         9   265
D3V7, multiclass
                                  clus
vv                                 ATRX MUTATED ATRX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              7
  BLACK OR AFRICAN AMERICAN                   6              9
  WHITE                                     173            265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                cls
clus               0   1
  ATRX MUTATED     8 162
  ATRX WILD-TYPE  10 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      8  162
  ATRX WILD-TYPE   10  258
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                8             10
  NOT HISPANIC OR LATINO          162            258
[1] 2 2
[1] FALSE

Clustering(4) Variable = CIC MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  CIC MUTATED    89  11
  CIC WILD-TYPE 289  82
  CIC MUTATED CIC WILD-TYPE 
          100           371 
  CIC MUTATED CIC WILD-TYPE 
           11            82 
$`CIC MUTATED`
TCGA-CS-5394 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-A4XA 
        0.10         8.02         6.61        75.25        50.17        18.84 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       24.20        30.12         5.98        31.40        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7UR 
       14.40        12.10        31.82         8.02        17.19        54.25 
TCGA-DH-A7US TCGA-DU-5870 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7018 
       13.12       182.33       211.17        52.11         1.22        30.67 
TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S8 
       94.32        60.30        14.17         8.65         2.70         5.98 
TCGA-DU-A7T6 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-EZ-7264 
       17.98       134.27        78.21        95.57        75.02        14.33 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-A60K 
       47.77        34.36        15.35        22.55        20.61        17.82 
TCGA-FG-A6IZ TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 
       15.02        36.66        20.45         6.67         0.13        75.19 
TCGA-HT-7602 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7694 
       29.85        22.06         0.23        16.24        44.68         6.90 
TCGA-HT-7695 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A4DV 
       14.53         0.33         0.13         9.40         6.25        26.04 
TCGA-HT-A5R9 TCGA-HT-A619 TCGA-HW-7487 TCGA-HW-7491 TCGA-IK-8125 TCGA-KT-A74X 
        0.07        21.40        19.89        40.18        42.77        14.40 
TCGA-P5-A5F0 TCGA-P5-A72Z TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY 
        4.11        11.64        12.62        15.85        14.04         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK 
        9.17        14.53        16.34        16.73        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TW 
       94.03        32.65        59.38        30.87         5.46        37.84 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       23.64        32.61       106.39        69.50        72.59        32.45 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-TM-A7C5 
       23.51         8.19         2.04        17.03        13.02        49.32 
TCGA-TM-A84M TCGA-TM-A84O TCGA-VM-A8CB TCGA-VM-A8CE 
       24.79        33.24         0.10        35.93 

$`CIC WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 
       17.95        12.43         8.48         7.56         7.40       122.73 
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 
       81.96        47.93        72.92        50.86        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        46.42        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X 
       33.57        72.95        31.63        25.48        27.45        18.51 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        30.31 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       14.40        30.21        42.05        27.81        17.19        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81        18.94        17.49        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       12.20        77.98         7.23        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 
       57.93       130.78        32.45        36.82        32.35         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
        0.20        25.48        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7643 TCGA-FG-8181 
       23.97        18.44        17.88        40.08        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        16.41        16.44        22.26        28.54        10.78 
TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 
       48.69        13.58         5.72        27.52         0.10        11.54 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38        40.34        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
        3.16        45.99        56.09        57.60        14.27         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
        0.10         0.10         2.96        17.52        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.23         0.13        20.22        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A 
        2.70        16.93         1.81        16.14        16.83         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 
        0.10        29.92         8.32        19.23         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.37         2.30         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.16        10.42        13.25         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.16         2.53        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A870 
       12.23        10.29         1.91        16.50         5.03        12.99 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        18.77        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG 
       17.62        16.08        98.24        95.93         5.85        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13         7.92        22.32         7.13        20.02 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        28.37       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q 
       40.64        30.44        28.08        24.16        40.83        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       30.08        13.51         7.89        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  CIC MUTATED CIC WILD-TYPE 
         0.07          0.03 
  CIC MUTATED CIC WILD-TYPE 
       211.17        172.77 
  CIC MUTATED CIC WILD-TYPE 
        20.17         18.51 
[1] "0.1 - 211.2 (20.2)" "0.0 - 172.8 (18.5)"
[1] "hr=" "2.4"
D4V2, continuous
D4V3, binary
               cls
clus              0   1
  CIC MUTATED    47  53
  CIC WILD-TYPE 160 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     47   53
  CIC WILD-TYPE  160  213
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE          47           160
  MALE            53           213
[1] 2 2
[1] FALSE
D4V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CIC MUTATED             3               20                77
  CIC WILD-TYPE         172               99               102
D4V5, multiclass
                   clus
vv                  CIC MUTATED CIC WILD-TYPE
  ASTROCYTOMA                 3           172
  OLIGOASTROCYTOMA           20            99
  OLIGODENDROGLIOMA          77           102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
               cls
clus              0   1
  CIC MUTATED    13  87
  CIC WILD-TYPE  79 294
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     13   87
  CIC WILD-TYPE   79  294
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           13            79
  YES          87           294
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIC MUTATED                                  0     2
  CIC WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CIC MUTATED                           2    93
  CIC WILD-TYPE                        13   345
D4V7, multiclass
                                  clus
vv                                 CIC MUTATED CIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             6
  BLACK OR AFRICAN AMERICAN                  2            13
  WHITE                                     93           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
               cls
clus              0   1
  CIC MUTATED     3  90
  CIC WILD-TYPE  15 330
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      3   90
  CIC WILD-TYPE   15  330
                        clus
vv                       CIC MUTATED CIC WILD-TYPE
  HISPANIC OR LATINO               3            15
  NOT HISPANIC OR LATINO          90           330
[1] 2 2
[1] FALSE

Clustering(5) Variable = NOTCH1 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    34   7
  NOTCH1 WILD-TYPE 344  86
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              41              430 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               7               86 
$`NOTCH1 MUTATED`
TCGA-CS-5390 TCGA-CS-6668 TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A75K TCGA-DH-5144 
       64.64         8.02        72.95        24.20        12.10         8.02 
TCGA-DH-A66B TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7300 
       42.05       211.17        22.42         1.22        30.67        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A6S3 TCGA-E1-5311 
       25.91        60.30        14.17        12.59         2.70       134.27 
TCGA-FG-5962 TCGA-FG-7638 TCGA-FG-8186 TCGA-FG-A710 TCGA-HT-7470 TCGA-HT-7481 
       47.77        22.55        16.01        36.66        40.11        95.93 
TCGA-HT-7875 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A616 TCGA-HW-8322 TCGA-HW-A5KJ 
        0.33         9.40         6.25         1.81        17.82        20.35 
TCGA-IK-8125 TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-R8-A6ML 
       42.77         4.11         7.63        13.61        10.29        94.03 
TCGA-S9-A6U5 TCGA-TM-A7CF TCGA-TM-A84G TCGA-VV-A829 TCGA-VW-A7QS 
       32.61        48.39        40.64        37.05        23.21 

$`NOTCH1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         8.48         7.56         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH 
       30.21        46.72        39.78        37.45        33.57        31.63 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       29.23        14.40        18.51        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 
       16.18        19.96        31.82        30.31        14.40        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        52.11        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       90.77        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       44.02        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        14.24        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        10.78        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38        40.34        75.19       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
       37.15         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64        16.24        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       21.60        19.59        12.76        20.81        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         5.88         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.53        12.23         2.20         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       17.62        23.64        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       34.78        24.92        16.18        59.05        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M 
       13.51         0.10         7.89        35.93        23.47        16.01 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.33             0.03 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          211.17           182.33 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           23.21            18.41 
[1] "0.3 - 211.2 (23.2)" "0.0 - 182.3 (18.4)"
[1] "hr=" "1.6"
D5V2, continuous
D5V3, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    20  22
  NOTCH1 WILD-TYPE 187 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     20   22
  NOTCH1 WILD-TYPE  187  244
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             20              187
  MALE               22              244
[1] 2 2
[1] FALSE
D5V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NOTCH1 MUTATED             6                7                29
  NOTCH1 WILD-TYPE         169              112               150
D5V5, multiclass
                   clus
vv                  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASTROCYTOMA                    6              169
  OLIGOASTROCYTOMA               7              112
  OLIGODENDROGLIOMA             29              150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     8  34
  NOTCH1 WILD-TYPE  84 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      8   34
  NOTCH1 WILD-TYPE   84  347
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO               8               84
  YES             34              347
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH1 MUTATED                                  0     1
  NOTCH1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED                           0    41
  NOTCH1 WILD-TYPE                        15   397
D5V7, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                7
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                        41              397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     2  38
  NOTCH1 WILD-TYPE  16 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      2   38
  NOTCH1 WILD-TYPE   16  382
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  2               16
  NOT HISPANIC OR LATINO             38              382
[1] 2 2
[1] FALSE

Clustering(6) Variable = EGFR MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    16  14
  EGFR WILD-TYPE 362  79
  EGFR MUTATED EGFR WILD-TYPE 
            30            441 
  EGFR MUTATED EGFR WILD-TYPE 
            14             79 
$`EGFR MUTATED`
TCGA-DU-5852 TCGA-DU-6392 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7292 
        6.74       211.17         7.96        11.47         6.54         7.96 
TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A7TD 
        5.10        14.60        21.40         4.96        12.20         7.50 
TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-8104 
       18.44        10.72        18.38        10.78         5.72        12.23 
TCGA-HT-8107 TCGA-HT-8110 TCGA-HT-A5RC TCGA-HT-A61C TCGA-KT-A7W1 TCGA-QH-A6CX 
        0.46        13.78         5.33        17.65        14.40        12.23 
TCGA-QH-A6XC TCGA-S9-A6WN TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-VM-A8CD 
        5.03        15.91        22.32        10.39        49.45         7.89 

$`EGFR WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 
       19.89        16.83        94.52       114.08         7.73        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99       105.21         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       30.67        26.30        10.36        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       23.74        20.68        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       14.24        12.59        15.12         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       23.51        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       14.93        24.99        23.97        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       13.58        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        9.40        63.55         0.10        37.87        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.10         2.50         5.56         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07        27.35         0.10         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        1.91        16.50        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        19.86        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  EGFR MUTATED EGFR WILD-TYPE 
          0.46           0.03 
  EGFR MUTATED EGFR WILD-TYPE 
        211.17         182.33 
  EGFR MUTATED EGFR WILD-TYPE 
        11.125         19.230 
[1] "0.5 - 211.2 (11.1)" "0.0 - 182.3 (19.2)"
[1] "hr=" "4.9"
D6V2, continuous
D6V3, binary
                cls
clus               0   1
  EGFR MUTATED    14  16
  EGFR WILD-TYPE 193 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     14   16
  EGFR WILD-TYPE  193  250
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           14            193
  MALE             16            250
[1] 2 2
[1] FALSE
D6V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EGFR MUTATED            18                6                 6
  EGFR WILD-TYPE         157              113               173
D6V5, multiclass
                   clus
vv                  EGFR MUTATED EGFR WILD-TYPE
  ASTROCYTOMA                 18            157
  OLIGOASTROCYTOMA             6            113
  OLIGODENDROGLIOMA            6            173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                cls
clus               0   1
  EGFR MUTATED     3  27
  EGFR WILD-TYPE  89 354
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      3   27
  EGFR WILD-TYPE   89  354
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO             3             89
  YES           27            354
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     0
  EGFR WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           2    28
  EGFR WILD-TYPE                        13   410
D6V7, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   2             13
  WHITE                                      28            410
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                cls
clus               0   1
  EGFR MUTATED     0  29
  EGFR WILD-TYPE  18 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   29
  EGFR WILD-TYPE   18  391
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO           29            391
[1] 2 2
[1] FALSE

Clustering(7) Variable = PIK3R1 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    16   3
  PIK3R1 WILD-TYPE 362  90
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              19              452 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               3               90 
$`PIK3R1 MUTATED`
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6188 TCGA-DB-5279 TCGA-DU-5870 
       43.89        10.62         0.10        23.84        44.52       182.33 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-7300 TCGA-DU-A7TB TCGA-DU-A7TJ TCGA-FG-5962 
      211.17        22.42        62.01        42.31         0.56        47.77 
TCGA-FG-8188 TCGA-HT-7481 TCGA-HT-7694 TCGA-HT-A74K TCGA-KT-A74X TCGA-QH-A6X8 
       14.96        95.93         6.90        15.35        14.40        16.73 
TCGA-S9-A7IY 
       23.51 

$`PIK3R1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5395 
        4.70         7.69        18.15        64.64        40.18        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        9.96         6.38        17.69        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 
       75.25        47.93        72.92        50.86        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       37.45        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       14.40        18.51        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 
       17.46         6.74        13.38         8.45         6.81        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 
        7.96        94.32        18.94        44.02        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
       77.88        23.51         7.50        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        20.09        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       40.34        75.19       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
       17.52        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
       17.65         2.43        10.52        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13         7.92        22.32         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.10             0.03 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          211.17           172.77 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           23.51            18.56 
[1] "0.1 - 211.2 (23.5)" "0.0 - 172.8 (18.6)"
[1] "hr=" "2.4"
D7V2, continuous
D7V3, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     6  14
  PIK3R1 WILD-TYPE 201 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      6   14
  PIK3R1 WILD-TYPE  201  252
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              6              201
  MALE               14              252
[1] 2 2
[1] FALSE
D7V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PIK3R1 MUTATED             7                3                10
  PIK3R1 WILD-TYPE         168              116               169
D7V5, multiclass
                   clus
vv                  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASTROCYTOMA                    7              168
  OLIGOASTROCYTOMA               3              116
  OLIGODENDROGLIOMA             10              169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     7  13
  PIK3R1 WILD-TYPE  85 368
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      7   13
  PIK3R1 WILD-TYPE   85  368
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               7               85
  YES             13              368
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  0     1
  PIK3R1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED                           2    16
  PIK3R1 WILD-TYPE                        13   422
D7V7, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                7
  BLACK OR AFRICAN AMERICAN                     2               13
  WHITE                                        16              422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     0  16
  PIK3R1 WILD-TYPE  18 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0   16
  PIK3R1 WILD-TYPE   18  404
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO             16              404
[1] 2 2
[1] FALSE

Clustering(8) Variable = IDH2 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED    18   1
  IDH2 WILD-TYPE 360  92
  IDH2 MUTATED IDH2 WILD-TYPE 
            19            452 
  IDH2 MUTATED IDH2 WILD-TYPE 
             1             92 
$`IDH2 MUTATED`
TCGA-DB-A4XG TCGA-DH-5141 TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-7309 TCGA-DU-A7TA 
       72.95        31.82        54.25        14.56         2.76        77.88 
TCGA-E1-5318 TCGA-FG-8189 TCGA-HT-7476 TCGA-HT-7681 TCGA-HT-7856 TCGA-HT-8113 
       78.21        22.52         6.54        44.68        39.09        29.59 
TCGA-HT-A5R9 TCGA-HW-7491 TCGA-P5-A730 TCGA-QH-A65X TCGA-S9-A6TY TCGA-S9-A7QY 
        0.07        40.18         0.20        15.85        31.33        28.37 
TCGA-TM-A84R 
       18.61 

$`IDH2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        21.30        17.98       124.50        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       79.99        57.93       134.27        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        14.96        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
       16.24         0.76         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        19.23         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13        20.22        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       10.42        13.25        11.64         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       62.17        87.12        18.77        37.84        34.49        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       13.12        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       33.24        25.38        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  IDH2 MUTATED IDH2 WILD-TYPE 
          0.07           0.03 
  IDH2 MUTATED IDH2 WILD-TYPE 
         78.21         211.17 
  IDH2 MUTATED IDH2 WILD-TYPE 
         29.59          18.41 
[1] "0.1 - 78.2 (29.6)"  "0.0 - 211.2 (18.4)"
[1] "hr=" "4.4"
D8V2, continuous
D8V3, binary
                cls
clus               0   1
  IDH2 MUTATED     9  10
  IDH2 WILD-TYPE 198 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      9   10
  IDH2 WILD-TYPE  198  256
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE            9            198
  MALE             10            256
[1] 2 2
[1] FALSE
D8V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IDH2 MUTATED             1                4                14
  IDH2 WILD-TYPE         174              115               165
D8V5, multiclass
                   clus
vv                  IDH2 MUTATED IDH2 WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             4            115
  OLIGODENDROGLIOMA           14            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                cls
clus               0   1
  IDH2 MUTATED     4  15
  IDH2 WILD-TYPE  88 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      4   15
  IDH2 WILD-TYPE   88  366
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO             4             88
  YES           15            366
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH2 MUTATED                                  0     0
  IDH2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED                           1    18
  IDH2 WILD-TYPE                        14   420
D8V7, multiclass
                                  clus
vv                                 IDH2 MUTATED IDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   1             14
  WHITE                                      18            420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                cls
clus               0   1
  IDH2 MUTATED     2  16
  IDH2 WILD-TYPE  16 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      2   16
  IDH2 WILD-TYPE   16  404
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                2             16
  NOT HISPANIC OR LATINO           16            404
[1] 2 2
[1] FALSE

Clustering(9) Variable = NF1 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    17  14
  NF1 WILD-TYPE 361  79
  NF1 MUTATED NF1 WILD-TYPE 
           31           440 
  NF1 MUTATED NF1 WILD-TYPE 
           14            79 
$`NF1 MUTATED`
TCGA-CS-5397 TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A75K TCGA-DH-5140 TCGA-DU-5847 
        6.38        72.95        25.48        12.10        19.96        18.02 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6402 TCGA-DU-7006 TCGA-DU-7299 
      211.17        22.42        46.06         7.04        11.47        44.02 
TCGA-DU-A76L TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-A87N TCGA-HT-7608 TCGA-HT-7857 
       26.76        25.48        18.77        13.58        22.06         0.23 
TCGA-HT-7860 TCGA-HT-7880 TCGA-HT-8010 TCGA-HT-8564 TCGA-HT-A4DS TCGA-QH-A6CS 
        0.49         5.33         1.64        15.72         0.23        19.33 
TCGA-QH-A6CX TCGA-S9-A6UA TCGA-S9-A6WP TCGA-S9-A7IX TCGA-S9-A89V TCGA-TM-A84C 
       12.23         5.85        15.16        22.32        18.71        16.18 
TCGA-VM-A8CD 
        7.89 

$`NF1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        24.20        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        14.40        18.51        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       13.12        13.38         3.45        18.61        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       17.49        15.16        52.11        49.02        75.16        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22        87.45        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A76R 
       77.98         7.23         5.98        11.41         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       47.77        34.36        36.82        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57        17.29         3.16        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       39.48        19.23        39.09        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         3.68        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       28.27        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY 
       15.85        14.04        14.83        14.53        13.61         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       23.64        32.61        16.08        98.24        95.93       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       19.86        15.91        18.61        14.07        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       99.06        30.05        98.63        31.59        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        24.92        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       26.99        43.04        30.08        13.51         0.10        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  NF1 MUTATED NF1 WILD-TYPE 
         0.23          0.03 
  NF1 MUTATED NF1 WILD-TYPE 
       211.17        182.33 
  NF1 MUTATED NF1 WILD-TYPE 
        16.18         18.66 
[1] "0.2 - 211.2 (16.2)" "0.0 - 182.3 (18.7)"
[1] "hr=" "3.3"
D9V2, continuous
D9V3, binary
               cls
clus              0   1
  NF1 MUTATED    12  19
  NF1 WILD-TYPE 195 247
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     12   19
  NF1 WILD-TYPE  195  247
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          12           195
  MALE            19           247
[1] 2 2
[1] FALSE
D9V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NF1 MUTATED            20                6                 5
  NF1 WILD-TYPE         155              113               174
D9V5, multiclass
                   clus
vv                  NF1 MUTATED NF1 WILD-TYPE
  ASTROCYTOMA                20           155
  OLIGOASTROCYTOMA            6           113
  OLIGODENDROGLIOMA           5           174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
               cls
clus              0   1
  NF1 MUTATED    10  21
  NF1 WILD-TYPE  82 360
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     10   21
  NF1 WILD-TYPE   82  360
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           10            82
  YES          21           360
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     1
  NF1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           2    28
  NF1 WILD-TYPE                        13   410
D9V7, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             7
  BLACK OR AFRICAN AMERICAN                  2            13
  WHITE                                     28           410
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
               cls
clus              0   1
  NF1 MUTATED     2  28
  NF1 WILD-TYPE  16 392
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      2   28
  NF1 WILD-TYPE   16  392
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               2            16
  NOT HISPANIC OR LATINO          28           392
[1] 2 2
[1] FALSE

Clustering(10) Variable = PTEN MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    12  11
  PTEN WILD-TYPE 366  82
  PTEN MUTATED PTEN WILD-TYPE 
            23            448 
  PTEN MUTATED PTEN WILD-TYPE 
            11             82 
$`PTEN MUTATED`
TCGA-CS-5395 TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-6392 TCGA-DU-6402 
       21.01         3.45        18.61        18.02       211.17         7.04 
TCGA-DU-7012 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-A7TD TCGA-FG-6692 TCGA-FG-A4MW 
        6.54        10.36         5.10         7.50        18.44        18.38 
TCGA-HT-7860 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-A5RA TCGA-QH-A6CS TCGA-QH-A6CX 
        0.49        16.24        12.23        27.35        19.33        12.23 
TCGA-QH-A6X3 TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-TM-A84B TCGA-VM-A8CD 
       10.29        37.84        22.95        24.92         7.89 

$`PTEN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99       105.21         8.84        90.77        30.67        26.30 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       77.88        42.31        23.51        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       36.82        18.77        14.93        24.99        23.97        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       32.61        38.27        10.72        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        15.85        14.04        14.83        14.53        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20         9.17        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        28.70        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        0.10        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  PTEN MUTATED PTEN WILD-TYPE 
          0.49           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
        211.17         182.33 
  PTEN MUTATED PTEN WILD-TYPE 
         16.24          18.77 
[1] "0.5 - 211.2 (16.2)" "0.0 - 182.3 (18.8)"
[1] "hr=" "3.7"
D10V2, continuous
D10V3, binary
                cls
clus               0   1
  PTEN MUTATED     8  15
  PTEN WILD-TYPE 199 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8   15
  PTEN WILD-TYPE  199  251
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            8            199
  MALE             15            251
[1] 2 2
[1] FALSE
D10V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PTEN MUTATED            17                3                 3
  PTEN WILD-TYPE         158              116               176
D10V5, multiclass
                   clus
vv                  PTEN MUTATED PTEN WILD-TYPE
  ASTROCYTOMA                 17            158
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            3            176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                cls
clus               0   1
  PTEN MUTATED     6  17
  PTEN WILD-TYPE  86 364
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6   17
  PTEN WILD-TYPE   86  364
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             6             86
  YES           17            364
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           2    21
  PTEN WILD-TYPE                        13   417
D10V7, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   2             13
  WHITE                                      21            417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                cls
clus               0   1
  PTEN MUTATED     0  21
  PTEN WILD-TYPE  18 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   21
  PTEN WILD-TYPE   18  399
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO           21            399
[1] 2 2
[1] FALSE

Clustering(11) Variable = FUBP1 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  FUBP1 MUTATED    40   6
  FUBP1 WILD-TYPE 338  87
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             46             425 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
              6              87 
$`FUBP1 MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-DB-5274 TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V 
       64.64         0.10        75.25        24.20         5.98        29.23 
TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A7UR TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6397 
       12.10         8.02        54.25       211.17        22.42        46.06 
TCGA-DU-7300 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-E1-5319 
       62.01        21.40        14.17         8.65         2.70        95.57 
TCGA-E1-A7YO TCGA-EZ-7264 TCGA-FG-A710 TCGA-HT-7467 TCGA-HT-7471 TCGA-HT-7481 
       75.02        14.33        36.66         0.10         0.13        95.93 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7694 TCGA-HT-8105 
       22.06         0.23        14.27        16.24         6.90         6.25 
TCGA-HT-A615 TCGA-HW-7487 TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A86X TCGA-RY-A83Y 
       16.93        19.89         9.17        14.53        11.08         5.46 
TCGA-RY-A847 TCGA-S9-A6TX TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J3 
       30.67        34.49        15.16        23.51         8.19        17.03 
TCGA-S9-A7QZ TCGA-TM-A84G TCGA-TM-A84M TCGA-VM-A8CB 
       13.02        40.64        24.79         0.10 

$`FUBP1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
      122.73        81.96        47.93        72.92        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W 
       25.48        30.12        31.40        27.45        27.81        14.40 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       12.20        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 
       41.13        79.99        57.93       134.27        78.21       130.78 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       32.45        36.82        32.35         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 
       15.02        16.44        22.26        28.54        10.78        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7469 
       20.45        13.58         5.72        27.52         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38        40.34        75.19       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 
       17.29         3.16        45.99        56.09        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7695 
       14.96         0.10         0.10         2.96        17.52        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        5.33         2.70         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       11.05         0.10        29.92         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
       14.83        14.53        13.61        12.23         2.20        10.29 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A870 
       16.34        16.73         1.91        16.50         5.03        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Z 
       88.83        94.03        32.65        59.38        30.87         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       37.84        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       19.86        15.91        18.61        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX 
       22.32         7.13        20.02         2.04        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       34.78        48.39        24.92        16.18        59.05        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        24.16        40.83        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       13.51         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  FUBP1 MUTATED FUBP1 WILD-TYPE 
           0.10            0.03 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
         211.17          182.33 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
         16.585          18.710 
[1] "0.1 - 211.2 (16.6)" "0.0 - 182.3 (18.7)"
[1] "hr=" "1.6"
D11V2, continuous
D11V3, binary
                 cls
clus                0   1
  FUBP1 MUTATED    18  28
  FUBP1 WILD-TYPE 189 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED     18   28
  FUBP1 WILD-TYPE  189  238
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  FEMALE            18             189
  MALE              28             238
[1] 2 2
[1] FALSE
D11V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FUBP1 MUTATED             2                8                36
  FUBP1 WILD-TYPE         173              111               143
D11V5, multiclass
                   clus
vv                  FUBP1 MUTATED FUBP1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              8             111
  OLIGODENDROGLIOMA            36             143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                 cls
clus                0   1
  FUBP1 MUTATED     9  37
  FUBP1 WILD-TYPE  83 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED      9   37
  FUBP1 WILD-TYPE   83  344
     clus
vv    FUBP1 MUTATED FUBP1 WILD-TYPE
  NO              9              83
  YES            37             344
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUBP1 MUTATED                                  0     0
  FUBP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUBP1 MUTATED                           2    42
  FUBP1 WILD-TYPE                        13   396
D11V7, multiclass
                                  clus
vv                                 FUBP1 MUTATED FUBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    2              13
  WHITE                                       42             396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                 cls
clus                0   1
  FUBP1 MUTATED     0  42
  FUBP1 WILD-TYPE  18 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED      0   42
  FUBP1 WILD-TYPE   18  378
                        clus
vv                       FUBP1 MUTATED FUBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            42             378
[1] 2 2
[1] FALSE

Clustering(12) Variable = ARID1A MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    18   1
  ARID1A WILD-TYPE 360  92
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              452 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               92 
$`ARID1A MUTATED`
TCGA-DB-5275 TCGA-DB-A4XA TCGA-DU-6392 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7304 
       47.93        18.84       211.17         7.96       138.28        23.31 
TCGA-FG-5962 TCGA-FG-7637 TCGA-FG-A60L TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7611 
       47.77        40.08        16.41        36.66         6.67        57.60 
TCGA-HT-7688 TCGA-HT-8564 TCGA-HW-7490 TCGA-QH-A65X TCGA-S9-A6U2 TCGA-TM-A84M 
       31.69        15.72        19.23        15.85        23.64        24.79 
TCGA-TM-A84S 
       14.93 

$`ARID1A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        75.25        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83        94.52       114.08         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       44.02        62.01        25.91        60.30        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ 
       18.38        18.71        23.70        14.76        17.82        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        10.78        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 
       13.58         5.72        27.52         0.10        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        13.74        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 
        0.10        29.92        19.89         8.32        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       28.70        22.95        17.62        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       33.24        25.38        18.61        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.67             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
          211.17           182.33 
  ARID1A MUTATED ARID1A WILD-TYPE 
           23.64            18.41 
[1] "6.7 - 211.2 (23.6)" "0.0 - 182.3 (18.4)"
[1] "hr=" "6.3"
D12V2, continuous
D12V3, binary
                  cls
clus                 0   1
  ARID1A MUTATED     6  13
  ARID1A WILD-TYPE 201 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6   13
  ARID1A WILD-TYPE  201  253
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              6              201
  MALE               13              253
[1] 2 2
[1] FALSE
D12V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ARID1A MUTATED             4                6                 9
  ARID1A WILD-TYPE         171              113               170
D12V5, multiclass
                   clus
vv                  ARID1A MUTATED ARID1A WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               6              113
  OLIGODENDROGLIOMA              9              170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED     4  15
  ARID1A WILD-TYPE  88 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4   15
  ARID1A WILD-TYPE   88  366
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               4               88
  YES             15              366
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     0
  ARID1A WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           0    19
  ARID1A WILD-TYPE                        15   419
D12V7, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                        19              419
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  18
  ARID1A WILD-TYPE  17 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   18
  ARID1A WILD-TYPE   17  402
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             18              402
[1] 2 2
[1] FALSE

Clustering(13) Variable = PIK3CA MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    33   9
  PIK3CA WILD-TYPE 345  84
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              42              429 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               84 
$`PIK3CA MUTATED`
TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A64W TCGA-DU-6392 TCGA-DU-6405 TCGA-DU-7006 
        5.98        29.23        14.40       211.17        19.89        11.47 
TCGA-DU-7018 TCGA-DU-7298 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT 
       30.67        18.94        21.40        19.13        14.17         4.96 
TCGA-DU-A6S3 TCGA-DU-A76R TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-8187 TCGA-HT-7468 
        2.70        21.30        47.77        15.35        20.09         6.67 
TCGA-HT-7478 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7620 TCGA-HT-7692 
        6.38        95.93         4.57         3.16        14.27         2.96 
TCGA-HT-7874 TCGA-HT-7882 TCGA-HW-7491 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U 
       37.15         3.72        40.18        14.40         4.11         0.16 
TCGA-R8-A6MO TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6WN TCGA-S9-A7J1 
       32.65        37.84        22.95        23.64        15.91         8.19 
TCGA-S9-A7R7 TCGA-TM-A84F TCGA-TM-A84S TCGA-VM-A8C9 TCGA-VW-A8FI TCGA-WY-A85E 
       98.63        59.05        14.93        30.08         8.05        20.81 

$`PIK3CA WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       31.40        27.45        27.81        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04        11.64       133.74        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 
       14.99       105.21         6.54         8.84        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       14.60        20.68        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 
       15.12         3.65         5.65        12.20         8.65        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 
        7.23         5.98        11.41        26.76         7.13        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72        27.52         0.10        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       40.34        75.19       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
       29.85        23.18       122.47        17.29        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60         0.23         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 
        0.10        29.92        19.89         8.32        19.23         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         2.30         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       94.03        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 
       34.49        31.33        28.70        17.62        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO 
       80.12        32.45        84.99        31.10        19.86        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        7.13        20.02         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H 
       34.78        48.39        24.92        16.18        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.61        23.80        15.98        26.99        43.04        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.16             0.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          211.17           182.33 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          17.425           18.610 
[1] "0.2 - 211.2 (17.4)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    18  24
  PIK3CA WILD-TYPE 189 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     18   24
  PIK3CA WILD-TYPE  189  242
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             18              189
  MALE               24              242
[1] 2 2
[1] FALSE
D13V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PIK3CA MUTATED            13                5                24
  PIK3CA WILD-TYPE         162              114               155
D13V5, multiclass
                   clus
vv                  PIK3CA MUTATED PIK3CA WILD-TYPE
  ASTROCYTOMA                   13              162
  OLIGOASTROCYTOMA               5              114
  OLIGODENDROGLIOMA             24              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7  35
  PIK3CA WILD-TYPE  85 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7   35
  PIK3CA WILD-TYPE   85  346
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               7               85
  YES             35              346
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     1
  PIK3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           1    38
  PIK3CA WILD-TYPE                        14   400
D13V7, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                7
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                        38              400
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  36
  PIK3CA WILD-TYPE  17 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   36
  PIK3CA WILD-TYPE   17  384
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             36              384
[1] 2 2
[1] FALSE

Clustering(14) Variable = STK19 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     9   1
  STK19 WILD-TYPE 369  92
  STK19 MUTATED STK19 WILD-TYPE 
             10             461 
  STK19 MUTATED STK19 WILD-TYPE 
              1              92 
$`STK19 MUTATED`
TCGA-DU-6392 TCGA-FG-A60J TCGA-HT-8015 TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB 
      211.17        14.76         0.10         0.13        27.35         0.10 
TCGA-HT-A5RC TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-S9-A7QY 
        5.33         5.88         7.63        28.37 

$`STK19 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27        15.72         0.23        26.04        20.22         0.07 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         4.11         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        15.06        13.12        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  STK19 MUTATED STK19 WILD-TYPE 
           0.10            0.03 
  STK19 MUTATED STK19 WILD-TYPE 
         211.17          182.33 
  STK19 MUTATED STK19 WILD-TYPE 
          6.755          18.710 
[1] "0.1 - 211.2 (6.8)"  "0.0 - 182.3 (18.7)"
[1] "hr=" "2.2"
D14V2, continuous
D14V3, binary
                 cls
clus                0   1
  STK19 MUTATED     7   3
  STK19 WILD-TYPE 200 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      7    3
  STK19 WILD-TYPE  200  263
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             7             200
  MALE               3             263
[1] 2 2
[1] FALSE
D14V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  STK19 MUTATED             7                2                 1
  STK19 WILD-TYPE         168              117               178
D14V5, multiclass
                   clus
vv                  STK19 MUTATED STK19 WILD-TYPE
  ASTROCYTOMA                   7             168
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                 cls
clus                0   1
  STK19 MUTATED     1   9
  STK19 WILD-TYPE  91 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      1    9
  STK19 WILD-TYPE   91  372
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              1              91
  YES             9             372
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK19 MUTATED                                  0     0
  STK19 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED                           0    10
  STK19 WILD-TYPE                        15   428
D14V7, multiclass
                                  clus
vv                                 STK19 MUTATED STK19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                       10             428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                 cls
clus                0   1
  STK19 MUTATED     2   8
  STK19 WILD-TYPE  16 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    8
  STK19 WILD-TYPE   16  412
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO             8             412
[1] 2 2
[1] FALSE

Clustering(15) Variable = NIPBL MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED    17   0
  NIPBL WILD-TYPE 361  93
  NIPBL MUTATED NIPBL WILD-TYPE 
             17             454 
  NIPBL MUTATED NIPBL WILD-TYPE 
              0              93 
$`NIPBL MUTATED`
TCGA-DB-A4XG TCGA-DH-5141 TCGA-DH-A7UT TCGA-DU-6392 TCGA-DU-7009 TCGA-F6-A8O3 
       72.95        31.82        13.38       211.17       138.28         0.23 
TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-A619 TCGA-P5-A72Z TCGA-P5-A730 TCGA-R8-A6ML 
       27.52         6.67        21.40        11.64         0.20        94.03 
TCGA-RY-A83Y TCGA-S9-A6UB TCGA-S9-A7IY TCGA-TM-A7C3 TCGA-W9-A837 
        5.46       106.39        23.51        49.45        51.06 

$`NIPBL WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        13.12         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HT-A61B 
       16.93         1.81        16.14        16.83         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       13.25         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Z TCGA-RY-A840 
       88.83        32.65        59.38        30.87         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        22.32         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21         8.05        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  NIPBL MUTATED NIPBL WILD-TYPE 
           0.20            0.03 
  NIPBL MUTATED NIPBL WILD-TYPE 
         211.17          182.33 
  NIPBL MUTATED NIPBL WILD-TYPE 
         27.520          18.475 
[1] "0.2 - 211.2 (27.5)" "0.0 - 182.3 (18.5)"
[1] "hr="     "7.9e+07"
D15V2, continuous
D15V3, binary
                 cls
clus                0   1
  NIPBL MUTATED     5  12
  NIPBL WILD-TYPE 202 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      5   12
  NIPBL WILD-TYPE  202  254
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE             5             202
  MALE              12             254
[1] 2 2
[1] FALSE
D15V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NIPBL MUTATED             3                3                11
  NIPBL WILD-TYPE         172              116               168
D15V5, multiclass
                   clus
vv                  NIPBL MUTATED NIPBL WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA            11             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                 cls
clus                0   1
  NIPBL MUTATED     2  15
  NIPBL WILD-TYPE  90 366
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      2   15
  NIPBL WILD-TYPE   90  366
     clus
vv    NIPBL MUTATED NIPBL WILD-TYPE
  NO              2              90
  YES            15             366
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPBL MUTATED                                  0     2
  NIPBL WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPBL MUTATED                           0    15
  NIPBL WILD-TYPE                        15   423
D15V7, multiclass
                                  clus
vv                                 NIPBL MUTATED NIPBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               6
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                       15             423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                 cls
clus                0   1
  NIPBL MUTATED     2  15
  NIPBL WILD-TYPE  16 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      2   15
  NIPBL WILD-TYPE   16  405
                        clus
vv                       NIPBL MUTATED NIPBL WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO            15             405
[1] 2 2
[1] FALSE

Clustering(16) Variable = CREBZF MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2                0   1
  CREBZF MUTATED     5   1
  CREBZF WILD-TYPE 373  92
  CREBZF MUTATED CREBZF WILD-TYPE 
               6              465 
  CREBZF MUTATED CREBZF WILD-TYPE 
               1               92 
$`CREBZF MUTATED`
TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-8168 TCGA-DU-A6S3 TCGA-HT-7694 TCGA-P5-A5EX 
       18.94        60.30        14.17         2.70         6.90         1.64 

$`CREBZF WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7695 
       14.96         0.10         0.10         2.96        17.52        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  CREBZF MUTATED CREBZF WILD-TYPE 
            1.64             0.03 
  CREBZF MUTATED CREBZF WILD-TYPE 
           60.30           211.17 
  CREBZF MUTATED CREBZF WILD-TYPE 
          10.535           18.610 
[1] "1.6 - 60.3 (10.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.6"
D16V2, continuous
D16V3, binary
                  cls
clus                 0   1
  CREBZF MUTATED     4   2
  CREBZF WILD-TYPE 203 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      4    2
  CREBZF WILD-TYPE  203  264
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  FEMALE              4              203
  MALE                2              264
[1] 2 2
[1] FALSE
D16V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CREBZF MUTATED             1                0                 5
  CREBZF WILD-TYPE         174              119               174
D16V5, multiclass
                   clus
vv                  CREBZF MUTATED CREBZF WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              5              174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                  cls
clus                 0   1
  CREBZF MUTATED     1   5
  CREBZF WILD-TYPE  91 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      1    5
  CREBZF WILD-TYPE   91  376
     clus
vv    CREBZF MUTATED CREBZF WILD-TYPE
  NO               1               91
  YES              5              376
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREBZF MUTATED                                  0     0
  CREBZF WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CREBZF MUTATED                           1     5
  CREBZF WILD-TYPE                        14   433
D16V7, multiclass
                                  clus
vv                                 CREBZF MUTATED CREBZF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                         5              433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                  cls
clus                 0   1
  CREBZF MUTATED     0   6
  CREBZF WILD-TYPE  18 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      0    6
  CREBZF WILD-TYPE   18  414
                        clus
vv                       CREBZF MUTATED CREBZF WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              6              414
[1] 2 2
[1] FALSE

Clustering(17) Variable = TCF12 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  TCF12 MUTATED    12   3
  TCF12 WILD-TYPE 366  90
  TCF12 MUTATED TCF12 WILD-TYPE 
             15             456 
  TCF12 MUTATED TCF12 WILD-TYPE 
              3              90 
$`TCF12 MUTATED`
TCGA-CS-6668 TCGA-DB-5270 TCGA-DB-A75O TCGA-DU-7018 TCGA-E1-5307 TCGA-E1-A7YW 
        8.02       122.73        30.74        30.67        57.93        36.82 
TCGA-FG-8182 TCGA-HT-7601 TCGA-HT-7875 TCGA-HT-8011 TCGA-HT-8105 TCGA-S9-A6TZ 
       13.68         5.03         0.33        16.24         6.25        28.70 
TCGA-S9-A6U2 TCGA-S9-A6WH TCGA-TM-A84F 
       23.64        32.45        59.05 

$`TCF12 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        6.61        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        75.02        32.45        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8185 
       40.08        22.55        20.61        20.09        12.95        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 
        0.23        50.63         0.49        23.61        37.15         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 
       87.12        18.77        37.84        34.49        31.33        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       17.62        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        80.12        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       48.39        24.92        16.18        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  TCF12 MUTATED TCF12 WILD-TYPE 
           0.33            0.03 
  TCF12 MUTATED TCF12 WILD-TYPE 
         122.73          211.17 
  TCF12 MUTATED TCF12 WILD-TYPE 
          28.70           18.56 
[1] "0.3 - 122.7 (28.7)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                 cls
clus                0   1
  TCF12 MUTATED     8   7
  TCF12 WILD-TYPE 199 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      8    7
  TCF12 WILD-TYPE  199  259
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  FEMALE             8             199
  MALE               7             259
[1] 2 2
[1] FALSE
D17V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TCF12 MUTATED             6                3                 6
  TCF12 WILD-TYPE         169              116               173
D17V5, multiclass
                   clus
vv                  TCF12 MUTATED TCF12 WILD-TYPE
  ASTROCYTOMA                   6             169
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA             6             173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                 cls
clus                0   1
  TCF12 MUTATED     1  14
  TCF12 WILD-TYPE  91 367
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      1   14
  TCF12 WILD-TYPE   91  367
     clus
vv    TCF12 MUTATED TCF12 WILD-TYPE
  NO              1              91
  YES            14             367
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCF12 MUTATED                                  0     0
  TCF12 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TCF12 MUTATED                           0    15
  TCF12 WILD-TYPE                        15   423
D17V7, multiclass
                                  clus
vv                                 TCF12 MUTATED TCF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                       15             423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                 cls
clus                0   1
  TCF12 MUTATED     0  15
  TCF12 WILD-TYPE  18 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      0   15
  TCF12 WILD-TYPE   18  405
                        clus
vv                       TCF12 MUTATED TCF12 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            15             405
[1] 2 2
[1] FALSE

Clustering(18) Variable = TRERF1 MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED     4   2
  TRERF1 WILD-TYPE 374  91
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               6              465 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               2               91 
$`TRERF1 MUTATED`
TCGA-CS-4938 TCGA-DU-6392 TCGA-E1-5307 TCGA-HT-7902 TCGA-S9-A6WN TCGA-TM-A84L 
        4.70       211.17        57.93        31.43        15.91        40.83 

$`TRERF1 WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
        0.56        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO 
       80.12        32.45        84.99        31.10        19.86        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84M 
       59.05        40.64        30.44        28.08        24.16        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
            4.70             0.03 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          211.17           182.33 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           36.13            18.61 
[1] "4.7 - 211.2 (36.1)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.3"
D18V2, continuous
D18V3, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     5   1
  TRERF1 WILD-TYPE 202 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      5    1
  TRERF1 WILD-TYPE  202  265
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE              5              202
  MALE                1              265
[1] 2 2
[1] FALSE
D18V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TRERF1 MUTATED             4                2                 0
  TRERF1 WILD-TYPE         171              117               179
D18V5, multiclass
                   clus
vv                  TRERF1 MUTATED TRERF1 WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              0              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     1   5
  TRERF1 WILD-TYPE  91 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      1    5
  TRERF1 WILD-TYPE   91  376
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO               1               91
  YES              5              376
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRERF1 MUTATED                                  0     0
  TRERF1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED                           0     6
  TRERF1 WILD-TYPE                        15   432
D18V7, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         6              432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     0   6
  TRERF1 WILD-TYPE  18 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      0    6
  TRERF1 WILD-TYPE   18  414
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              6              414
[1] 2 2
[1] FALSE

Clustering(19) Variable = SRPX MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  SRPX MUTATED     1   2
  SRPX WILD-TYPE 377  91
  SRPX MUTATED SRPX WILD-TYPE 
             3            468 
  SRPX MUTATED SRPX WILD-TYPE 
             2             91 
$`SRPX MUTATED`
TCGA-DH-5144 TCGA-DU-7006 TCGA-E1-5319 
        8.02        11.47        95.57 

$`SRPX WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
      134.27        78.21       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  SRPX MUTATED SRPX WILD-TYPE 
          8.02           0.03 
  SRPX MUTATED SRPX WILD-TYPE 
         95.57         211.17 
  SRPX MUTATED SRPX WILD-TYPE 
         11.47          18.61 
[1] "8.0 - 95.6 (11.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.3"
D19V2, continuous
D19V3, binary
                cls
clus               0   1
  SRPX MUTATED     3   0
  SRPX WILD-TYPE 204 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      3    0
  SRPX WILD-TYPE  204  266
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE            3            204
  MALE              0            266
[1] 2 2
[1] FALSE
D19V4, continuous
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-A66B     TCGA-DH-A66D     TCGA-DH-A66F 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU     TCGA-DH-A7UV 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853     TCGA-DU-5854 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871     TCGA-DU-5874 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404     TCGA-DU-6405 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410     TCGA-DU-7011 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018     TCGA-DU-7019 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299     TCGA-DU-7300 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304     TCGA-DU-7306 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161     TCGA-DU-8162 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167     TCGA-DU-8168 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS     TCGA-DU-A5TU 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6     TCGA-DU-A6S7 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6     TCGA-DU-A7T8 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC     TCGA-DU-A7TD 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311     TCGA-E1-5318 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5322     TCGA-E1-A7YO     TCGA-E1-A7YV     TCGA-E1-A7YW 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-A7Z6     TCGA-FG-5963     TCGA-FG-5965     TCGA-FG-6688 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-6689     TCGA-FG-6690     TCGA-FG-6691     TCGA-FG-7636 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-7638     TCGA-FG-8181     TCGA-FG-8185     TCGA-FG-8186 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189     TCGA-FG-A4MT 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J     TCGA-FG-A60L 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-A6J1     TCGA-FG-A6J3     TCGA-FG-A711     TCGA-FG-A713 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470     TCGA-HT-7475 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607     TCGA-HT-7609 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692     TCGA-HT-7693 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875     TCGA-HT-7884 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7     TCGA-HT-A5RA 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-A5RC     TCGA-HT-A615     TCGA-HT-A617     TCGA-HT-A618 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C     TCGA-HT-A74L 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1     TCGA-P5-A5EU 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX     TCGA-P5-A5F0 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6     TCGA-P5-A731 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V     TCGA-QH-A65X 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU     TCGA-QH-A6CV 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY     TCGA-QH-A6CZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5     TCGA-QH-A6X8 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC     TCGA-QH-A86X 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840     TCGA-RY-A845 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU     TCGA-S9-A6TV 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY     TCGA-S9-A6TZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2     TCGA-S9-A6U5 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA     TCGA-S9-A6UB 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG     TCGA-S9-A6WH 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM     TCGA-S9-A6WN 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ     TCGA-S9-A7IQ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SRPX MUTATED             1                0                 2
  SRPX WILD-TYPE         174              119               177
D19V5, multiclass
                   clus
vv                  SRPX MUTATED SRPX WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                cls
clus               0   1
  SRPX MUTATED     1   2
  SRPX WILD-TYPE  91 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    2
  SRPX WILD-TYPE   91  379
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO             1             91
  YES            2            379
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRPX MUTATED                                  0     0
  SRPX WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SRPX MUTATED                           0     3
  SRPX WILD-TYPE                        15   435
D19V7, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                cls
clus               0   1
  SRPX MUTATED     0   3
  SRPX WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0    3
  SRPX WILD-TYPE   18  417
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(20) Variable = SMARCA4 MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    23   1
  SMARCA4 WILD-TYPE 355  92
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               24               447 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                1                92 
$`SMARCA4 MUTATED`
TCGA-CS-5393 TCGA-CS-6667 TCGA-DH-A7US TCGA-DH-A7UV TCGA-DU-6392 TCGA-DU-7008 
       40.18         7.56        13.12        18.61       211.17       156.23 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-F6-A8O3 TCGA-FG-6690 TCGA-HT-7606 
       30.67        26.30        94.32         0.23        24.99        17.29 
TCGA-HT-7688 TCGA-HT-7855 TCGA-HT-8109 TCGA-HT-A614 TCGA-HW-8322 TCGA-QH-A6CV 
       31.69        19.23         5.56         2.70        17.82        14.53 
TCGA-QH-A6CW TCGA-RY-A840 TCGA-S9-A7R4 TCGA-TM-A84H TCGA-WY-A858 TCGA-WY-A85A 
       13.61        28.08        30.05        30.44        43.96        43.40 

$`SMARCA4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-5847 
       17.19        17.19        54.25        13.38         3.45        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 
      114.08         7.96         7.73        11.47        62.96       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7290 
       14.99       105.21         6.54         8.84        90.77        10.36 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        7.96        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       36.82        18.77        14.93        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        2.96        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        2.50        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        27.35         0.10         5.33        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       21.60        19.59        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY 
       15.85        14.04        19.33        14.83        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 
       32.65        59.38        30.87         5.46         9.90         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        10.39        99.06        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85B 
       23.21         8.05        51.06        13.32        39.88        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             0.23              0.03 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           211.17            182.33 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           25.645            18.440 
[1] "0.2 - 211.2 (25.6)" "0.0 - 182.3 (18.4)"
[1] "hr=" "7.1"
D20V2, continuous
D20V3, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     8  16
  SMARCA4 WILD-TYPE 199 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      8   16
  SMARCA4 WILD-TYPE  199  250
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE               8               199
  MALE                16               250
[1] 2 2
[1] FALSE
D20V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SMARCA4 MUTATED             9                5                10
  SMARCA4 WILD-TYPE         166              114               169
D20V5, multiclass
                   clus
vv                  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  ASTROCYTOMA                     9               166
  OLIGOASTROCYTOMA                5               114
  OLIGODENDROGLIOMA              10               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     8  16
  SMARCA4 WILD-TYPE  84 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      8   16
  SMARCA4 WILD-TYPE   84  365
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO                8                84
  YES              16               365
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     2
  SMARCA4 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           0    21
  SMARCA4 WILD-TYPE                        15   417
D20V7, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 6
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         21               417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     1  19
  SMARCA4 WILD-TYPE  17 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      1   19
  SMARCA4 WILD-TYPE   17  401
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              19               401
[1] 2 2
[1] FALSE

Clustering(21) Variable = EMG1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     6   1
  EMG1 WILD-TYPE 372  92
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            464 
  EMG1 MUTATED EMG1 WILD-TYPE 
             1             92 
$`EMG1 MUTATED`
TCGA-DB-A75K TCGA-DU-7304 TCGA-HT-7485 TCGA-HT-7677 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.10        23.31         4.01        16.24        16.34        16.73 
TCGA-S9-A7IZ 
        7.13 

$`EMG1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7602 
       75.19        95.93       106.95       172.77         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
       14.07        36.13         7.92        22.32        23.51        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  EMG1 MUTATED EMG1 WILD-TYPE 
          4.01           0.03 
  EMG1 MUTATED EMG1 WILD-TYPE 
         23.31         211.17 
  EMG1 MUTATED EMG1 WILD-TYPE 
         16.24          18.71 
[1] "4.0 - 23.3 (16.2)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.1"
D21V2, continuous
D21V3, binary
                cls
clus               0   1
  EMG1 MUTATED     4   3
  EMG1 WILD-TYPE 203 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    3
  EMG1 WILD-TYPE  203  263
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            4            203
  MALE              3            263
[1] 2 2
[1] FALSE
D21V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EMG1 MUTATED             2                3                 2
  EMG1 WILD-TYPE         173              116               177
D21V5, multiclass
                   clus
vv                  EMG1 MUTATED EMG1 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  EMG1 MUTATED     1   6
  EMG1 WILD-TYPE  91 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      1    6
  EMG1 WILD-TYPE   91  375
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             1             91
  YES            6            375
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     7
  EMG1 WILD-TYPE                        15   431
D21V7, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       7            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                cls
clus               0   1
  EMG1 MUTATED     0   7
  EMG1 WILD-TYPE  18 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    7
  EMG1 WILD-TYPE   18  413
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            7            413
[1] 2 2
[1] FALSE

Clustering(22) Variable = FAM47C MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  FAM47C MUTATED    16   2
  FAM47C WILD-TYPE 362  91
  FAM47C MUTATED FAM47C WILD-TYPE 
              18              453 
  FAM47C MUTATED FAM47C WILD-TYPE 
               2               91 
$`FAM47C MUTATED`
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-6392 TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8186 
       17.19        17.19       211.17        17.88        20.09        16.01 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7610 TCGA-IK-8125 TCGA-P5-A731 
       40.11         0.13        75.19        56.09        42.77         9.01 
TCGA-QH-A6CS TCGA-RY-A845 TCGA-S9-A6WE TCGA-S9-A7J3 TCGA-S9-A7R2 TCGA-WY-A859 
       19.33        19.59        72.59        17.03        10.39        39.88 

$`FAM47C WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       42.05        27.81        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       18.44        15.35        40.08        22.55        20.61        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7473 
       27.52         0.10         6.67        11.54         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.20        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       69.50        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 
       15.06        13.12        28.37        13.02       169.84        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        13.32        43.96        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  FAM47C MUTATED FAM47C WILD-TYPE 
            0.13             0.03 
  FAM47C MUTATED FAM47C WILD-TYPE 
          211.17           182.33 
  FAM47C MUTATED FAM47C WILD-TYPE 
           19.46            18.61 
[1] "0.1 - 211.2 (19.5)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.5"
D22V2, continuous
D22V3, binary
                  cls
clus                 0   1
  FAM47C MUTATED    10   8
  FAM47C WILD-TYPE 197 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     10    8
  FAM47C WILD-TYPE  197  258
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE             10              197
  MALE                8              258
[1] 2 2
[1] FALSE
D22V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FAM47C MUTATED             5                6                 7
  FAM47C WILD-TYPE         170              113               172
D22V5, multiclass
                   clus
vv                  FAM47C MUTATED FAM47C WILD-TYPE
  ASTROCYTOMA                    5              170
  OLIGOASTROCYTOMA               6              113
  OLIGODENDROGLIOMA              7              172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                  cls
clus                 0   1
  FAM47C MUTATED     4  14
  FAM47C WILD-TYPE  88 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      4   14
  FAM47C WILD-TYPE   88  367
     clus
vv    FAM47C MUTATED FAM47C WILD-TYPE
  NO               4               88
  YES             14              367
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM47C MUTATED                                  0     0
  FAM47C WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED                           0    18
  FAM47C WILD-TYPE                        15   420
D22V7, multiclass
                                  clus
vv                                 FAM47C MUTATED FAM47C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                        18              420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                  cls
clus                 0   1
  FAM47C MUTATED     1  16
  FAM47C WILD-TYPE  17 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1   16
  FAM47C WILD-TYPE   17  404
                        clus
vv                       FAM47C MUTATED FAM47C WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             16              404
[1] 2 2
[1] FALSE

Clustering(23) Variable = TNRC18 MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  TNRC18 MUTATED     6   4
  TNRC18 WILD-TYPE 372  89
  TNRC18 MUTATED TNRC18 WILD-TYPE 
              10              461 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4               89 
$`TNRC18 MUTATED`
TCGA-DB-A4XC TCGA-DB-A64W TCGA-DU-6392 TCGA-E1-5305 TCGA-HT-8011 TCGA-S9-A6U8 
       46.72        14.40       211.17        79.99        16.24        98.24 
TCGA-S9-A6U9 TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A84R 
       95.93        10.39        18.71        18.61 

$`TNRC18 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        41.13        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6UA 
       22.95        17.62        23.64        32.61        16.08         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02       169.84        99.06        30.05        98.63        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        25.38        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  TNRC18 MUTATED TNRC18 WILD-TYPE 
           10.39             0.03 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
          211.17           182.33 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
          32.715           18.510 
[1] "10.4 - 211.2 (32.7)" "0.0 - 182.3 (18.5)" 
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     2   8
  TNRC18 WILD-TYPE 205 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      2    8
  TNRC18 WILD-TYPE  205  258
        clus
vv       TNRC18 MUTATED TNRC18 WILD-TYPE
  FEMALE              2              205
  MALE                8              258
[1] 2 2
[1] FALSE
D23V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TNRC18 MUTATED             7                2                 1
  TNRC18 WILD-TYPE         168              117               178
D23V5, multiclass
                   clus
vv                  TNRC18 MUTATED TNRC18 WILD-TYPE
  ASTROCYTOMA                    7              168
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     1   9
  TNRC18 WILD-TYPE  91 372
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      1    9
  TNRC18 WILD-TYPE   91  372
     clus
vv    TNRC18 MUTATED TNRC18 WILD-TYPE
  NO               1               91
  YES              9              372
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNRC18 MUTATED                                  0     0
  TNRC18 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNRC18 MUTATED                           0    10
  TNRC18 WILD-TYPE                        15   428
D23V7, multiclass
                                  clus
vv                                 TNRC18 MUTATED TNRC18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                        10              428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     0  10
  TNRC18 WILD-TYPE  18 410
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      0   10
  TNRC18 WILD-TYPE   18  410
                        clus
vv                       TNRC18 MUTATED TNRC18 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO             10              410
[1] 2 2
[1] FALSE

Clustering(24) Variable = DNMT3A MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    10   0
  DNMT3A WILD-TYPE 368  93
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              461 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               0               93 
$`DNMT3A MUTATED`
TCGA-DU-6392 TCGA-DU-A5TS TCGA-FG-A710 TCGA-HT-7481 TCGA-HT-8564 TCGA-HW-8321 
      211.17        15.12        36.66        95.93        15.72        19.59 
TCGA-QH-A65X TCGA-S9-A7QW TCGA-S9-A89V TCGA-WH-A86K 
       15.85        15.06        18.71        13.32 

$`DNMT3A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 
       15.02        16.44        22.26        28.54        10.78        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        9.01        13.61        15.16         2.53        12.62        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04        17.03        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
           13.32             0.03 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
          211.17           182.33 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           17.28            18.61 
[1] "13.3 - 211.2 (17.3)" "0.0 - 182.3 (18.6)" 
[1] "hr="     "2.7e+07"
D24V2, continuous
D24V3, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     4   6
  DNMT3A WILD-TYPE 203 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      4    6
  DNMT3A WILD-TYPE  203  260
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              4              203
  MALE                6              260
[1] 2 2
[1] FALSE
D24V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DNMT3A MUTATED             6                1                 3
  DNMT3A WILD-TYPE         169              118               176
D24V5, multiclass
                   clus
vv                  DNMT3A MUTATED DNMT3A WILD-TYPE
  ASTROCYTOMA                    6              169
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     1   9
  DNMT3A WILD-TYPE  91 372
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    9
  DNMT3A WILD-TYPE   91  372
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               1               91
  YES              9              372
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT3A MUTATED                                  0     0
  DNMT3A WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED                           1     9
  DNMT3A WILD-TYPE                        14   429
D24V7, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                         9              429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     1   9
  DNMT3A WILD-TYPE  17 411
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    9
  DNMT3A WILD-TYPE   17  411
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              9              411
[1] 2 2
[1] FALSE

Clustering(25) Variable = HTRA2 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  HTRA2 MUTATED     5   0
  HTRA2 WILD-TYPE 373  93
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              5             466 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              0              93 
$`HTRA2 MUTATED`
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-S9-A7R3 
        0.07         0.10         5.88         1.28        99.06 

$`HTRA2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
       26.04         0.13        20.22        27.35         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        4.11         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  HTRA2 MUTATED HTRA2 WILD-TYPE 
           0.07            0.03 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
          99.06          211.17 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
           1.28           18.66 
[1] "0.1 - 99.1 (1.3)"   "0.0 - 211.2 (18.7)"
[1] "hr="     "3400000"
D25V2, continuous
D25V3, binary
                 cls
clus                0   1
  HTRA2 MUTATED     2   3
  HTRA2 WILD-TYPE 205 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      2    3
  HTRA2 WILD-TYPE  205  263
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  FEMALE             2             205
  MALE               3             263
[1] 2 2
[1] FALSE
D25V4, continuous
[1] "Remove cluster labels:" "HTRA2 MUTATED"         
clus
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-A61C      TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-KT-A7W1      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R4 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HTRA2 MUTATED             3                0                 2
  HTRA2 WILD-TYPE         172              119               177
D25V5, multiclass
                   clus
vv                  HTRA2 MUTATED HTRA2 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                 cls
clus                0   1
  HTRA2 MUTATED     0   5
  HTRA2 WILD-TYPE  92 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      0    5
  HTRA2 WILD-TYPE   92  376
     clus
vv    HTRA2 MUTATED HTRA2 WILD-TYPE
  NO              0              92
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTRA2 MUTATED                                  0     0
  HTRA2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTRA2 MUTATED                           0     5
  HTRA2 WILD-TYPE                        15   433
D25V7, multiclass
                                  clus
vv                                 HTRA2 MUTATED HTRA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                 cls
clus                0   1
  HTRA2 MUTATED     1   4
  HTRA2 WILD-TYPE  17 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      1    4
  HTRA2 WILD-TYPE   17  416
                        clus
vv                       HTRA2 MUTATED HTRA2 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(26) Variable = ZNF709 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  ZNF709 MUTATED     2   2
  ZNF709 WILD-TYPE 376  91
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              467 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               2               91 
$`ZNF709 MUTATED`
TCGA-HT-7470 TCGA-HT-7608 TCGA-HT-7620 TCGA-IK-7675 
       40.11        22.06        14.27        19.00 

$`ZNF709 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        11.54         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 
        3.16        45.99        56.09        57.60         0.23         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
           14.27             0.03 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           40.11           211.17 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           20.53            18.61 
[1] "14.3 - 40.1 (20.5)" "0.0 - 211.2 (18.6)"
[1] "hr=" "3.5"
D26V2, continuous
D26V3, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     0   4
  ZNF709 WILD-TYPE 207 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    4
  ZNF709 WILD-TYPE  207  262
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  FEMALE              0              207
  MALE                4              262
[1] 2 2
[1] FALSE
D26V4, continuous
[1] "Remove cluster labels:" "ZNF709 MUTATED"        
clus
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               2              267 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-A74L       TCGA-KT-A74X       TCGA-KT-A7W1       TCGA-P5-A5EU 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX       TCGA-P5-A5F0 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6       TCGA-P5-A731 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65X 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU       TCGA-QH-A6CV 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY       TCGA-QH-A6CZ 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5       TCGA-QH-A6X8 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC       TCGA-QH-A86X 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840       TCGA-RY-A845 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU       TCGA-S9-A6TV 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY       TCGA-S9-A6TZ 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2       TCGA-S9-A6U5 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA       TCGA-S9-A6UB 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG       TCGA-S9-A6WH 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM       TCGA-S9-A6WN 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ       TCGA-S9-A7IQ 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY       TCGA-S9-A7IZ 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2       TCGA-S9-A7J3 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY       TCGA-S9-A7QZ 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3       TCGA-S9-A7R4 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V       TCGA-S9-A89Z 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5       TCGA-TM-A7CA 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C       TCGA-TM-A84F 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I       TCGA-TM-A84J 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O       TCGA-TM-A84Q 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T       TCGA-TQ-A7RW 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD       TCGA-VM-A8CE 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZNF709 MUTATED             0                1                 3
  ZNF709 WILD-TYPE         175              118               176
D26V5, multiclass
                   clus
vv                  ZNF709 MUTATED ZNF709 WILD-TYPE
  ASTROCYTOMA                    0              175
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     3   1
  ZNF709 WILD-TYPE  89 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      3    1
  ZNF709 WILD-TYPE   89  380
     clus
vv    ZNF709 MUTATED ZNF709 WILD-TYPE
  NO               3               89
  YES              1              380
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF709 MUTATED                                  0     0
  ZNF709 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF709 MUTATED                           1     3
  ZNF709 WILD-TYPE                        14   435
D26V7, multiclass
                                  clus
vv                                 ZNF709 MUTATED ZNF709 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     1   3
  ZNF709 WILD-TYPE  17 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      1    3
  ZNF709 WILD-TYPE   17  417
                        clus
vv                       ZNF709 MUTATED ZNF709 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              3              417
[1] 2 2
[1] FALSE

Clustering(27) Variable = RBPJ MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  RBPJ MUTATED     6   1
  RBPJ WILD-TYPE 372  92
  RBPJ MUTATED RBPJ WILD-TYPE 
             7            464 
  RBPJ MUTATED RBPJ WILD-TYPE 
             1             92 
$`RBPJ MUTATED`
TCGA-DH-A7UR TCGA-DU-6410 TCGA-FG-5964 TCGA-HT-8106 TCGA-HT-A5R9 TCGA-S9-A6WL 
       54.25         7.96        34.36         0.10         0.07        31.10 
TCGA-S9-A7IS 
        7.92 

$`RBPJ WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        27.81        17.19        17.19        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
      133.74        19.89        16.83        94.52       114.08         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA 
       15.72         0.23        26.04         0.13        20.22        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  RBPJ MUTATED RBPJ WILD-TYPE 
          0.07           0.03 
  RBPJ MUTATED RBPJ WILD-TYPE 
         54.25         211.17 
  RBPJ MUTATED RBPJ WILD-TYPE 
          7.96          18.61 
[1] "0.1 - 54.2 (8.0)"   "0.0 - 211.2 (18.6)"
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
                cls
clus               0   1
  RBPJ MUTATED     3   4
  RBPJ WILD-TYPE 204 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      3    4
  RBPJ WILD-TYPE  204  262
        clus
vv       RBPJ MUTATED RBPJ WILD-TYPE
  FEMALE            3            204
  MALE              4            262
[1] 2 2
[1] FALSE
D27V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RBPJ MUTATED             3                0                 4
  RBPJ WILD-TYPE         172              119               175
D27V5, multiclass
                   clus
vv                  RBPJ MUTATED RBPJ WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            4            175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                cls
clus               0   1
  RBPJ MUTATED     1   6
  RBPJ WILD-TYPE  91 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      1    6
  RBPJ WILD-TYPE   91  375
     clus
vv    RBPJ MUTATED RBPJ WILD-TYPE
  NO             1             91
  YES            6            375
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBPJ MUTATED                                  0     0
  RBPJ WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBPJ MUTATED                           0     7
  RBPJ WILD-TYPE                        15   431
D27V7, multiclass
                                  clus
vv                                 RBPJ MUTATED RBPJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       7            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                cls
clus               0   1
  RBPJ MUTATED     0   7
  RBPJ WILD-TYPE  18 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      0    7
  RBPJ WILD-TYPE   18  413
                        clus
vv                       RBPJ MUTATED RBPJ WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            7            413
[1] 2 2
[1] FALSE

Clustering(28) Variable = NRAS MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 374  93
  NRAS MUTATED NRAS WILD-TYPE 
             4            467 
  NRAS MUTATED NRAS WILD-TYPE 
             0             93 
$`NRAS MUTATED`
TCGA-CS-5390 TCGA-S9-A7J0 TCGA-VM-A8CA TCGA-W9-A837 
       64.64        20.02        13.51        51.06 

$`NRAS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       36.13         7.92        22.32        23.51         7.13         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  NRAS MUTATED NRAS WILD-TYPE 
         13.51           0.03 
  NRAS MUTATED NRAS WILD-TYPE 
         64.64         211.17 
  NRAS MUTATED NRAS WILD-TYPE 
         35.54          18.61 
[1] "13.5 - 64.6 (35.5)" "0.0 - 211.2 (18.6)"
[1] "hr="     "9100000"
D28V2, continuous
D28V3, binary
                cls
clus               0   1
  NRAS MUTATED     2   2
  NRAS WILD-TYPE 205 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      2    2
  NRAS WILD-TYPE  205  264
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            2            205
  MALE              2            264
[1] 2 2
[1] FALSE
D28V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NRAS MUTATED             0                0                 4
  NRAS WILD-TYPE         175              119               175
D28V5, multiclass
                   clus
vv                  NRAS MUTATED NRAS WILD-TYPE
  ASTROCYTOMA                  0            175
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            4            175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                cls
clus               0   1
  NRAS MUTATED     1   3
  NRAS WILD-TYPE  91 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    3
  NRAS WILD-TYPE   91  378
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             1             91
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     0
  NRAS WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           0     3
  NRAS WILD-TYPE                        15   435
D28V7, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                cls
clus               0   1
  NRAS MUTATED     0   2
  NRAS WILD-TYPE  18 418
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    2
  NRAS WILD-TYPE   18  418
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            2            418
[1] 2 2
[1] FALSE

Clustering(29) Variable = ZNF292 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  ZNF292 MUTATED     8   5
  ZNF292 WILD-TYPE 370  88
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              13              458 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
               5               88 
$`ZNF292 MUTATED`
TCGA-CS-4942 TCGA-DB-A64W TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-7302 
       43.89        14.40       211.17        65.75         1.22        60.30 
TCGA-FG-A87N TCGA-HT-7607 TCGA-HT-7687 TCGA-IK-8125 TCGA-P5-A733 TCGA-S9-A6WD 
       13.58         3.16         0.10        42.77        13.61        69.50 
TCGA-S9-A6WP 
       15.16 

$`ZNF292 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 
       52.11        22.42        49.02        75.16        46.06        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        62.01        25.91        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 
       10.78        36.66        48.69        20.45         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        19.00        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       11.64         0.20         9.01        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93         5.85       106.39        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ 
       84.99        31.10        19.86        15.91        18.61        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  ZNF292 MUTATED ZNF292 WILD-TYPE 
            0.10             0.03 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
          211.17           182.33 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
           15.16            18.61 
[1] "0.1 - 211.2 (15.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     8   5
  ZNF292 WILD-TYPE 199 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      8    5
  ZNF292 WILD-TYPE  199  261
        clus
vv       ZNF292 MUTATED ZNF292 WILD-TYPE
  FEMALE              8              199
  MALE                5              261
[1] 2 2
[1] FALSE
D29V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZNF292 MUTATED             5                3                 5
  ZNF292 WILD-TYPE         170              116               174
D29V5, multiclass
                   clus
vv                  ZNF292 MUTATED ZNF292 WILD-TYPE
  ASTROCYTOMA                    5              170
  OLIGOASTROCYTOMA               3              116
  OLIGODENDROGLIOMA              5              174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     3  10
  ZNF292 WILD-TYPE  89 371
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      3   10
  ZNF292 WILD-TYPE   89  371
     clus
vv    ZNF292 MUTATED ZNF292 WILD-TYPE
  NO               3               89
  YES             10              371
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF292 MUTATED                                  0     1
  ZNF292 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF292 MUTATED                           1    11
  ZNF292 WILD-TYPE                        14   427
D29V7, multiclass
                                  clus
vv                                 ZNF292 MUTATED ZNF292 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                7
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                        11              427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     0  12
  ZNF292 WILD-TYPE  18 408
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      0   12
  ZNF292 WILD-TYPE   18  408
                        clus
vv                       ZNF292 MUTATED ZNF292 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO             12              408
[1] 2 2
[1] FALSE

Clustering(30) Variable = PTPN11 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED     5   2
  PTPN11 WILD-TYPE 373  91
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              464 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               2               91 
$`PTPN11 MUTATED`
TCGA-CS-5395 TCGA-FG-7641 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 TCGA-VM-A8C8 
       21.01        20.61        39.48         0.23         0.49        43.04 
TCGA-VW-A8FI 
        8.05 

$`PTPN11 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
       17.52         6.90        14.53        19.23        39.09        50.63 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
            0.23             0.03 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           43.04           211.17 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           20.61            18.61 
[1] "0.2 - 43.0 (20.6)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.4"
D30V2, continuous
D30V3, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     3   4
  PTPN11 WILD-TYPE 204 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      3    4
  PTPN11 WILD-TYPE  204  262
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE              3              204
  MALE                4              262
[1] 2 2
[1] FALSE
D30V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PTPN11 MUTATED             4                0                 3
  PTPN11 WILD-TYPE         171              119               176
D30V5, multiclass
                   clus
vv                  PTPN11 MUTATED PTPN11 WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     2   5
  PTPN11 WILD-TYPE  90 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      2    5
  PTPN11 WILD-TYPE   90  376
     clus
vv    PTPN11 MUTATED PTPN11 WILD-TYPE
  NO               2               90
  YES              5              376
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN11 MUTATED                                  0     0
  PTPN11 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN11 MUTATED                           1     6
  PTPN11 WILD-TYPE                        14   432
D30V7, multiclass
                                  clus
vv                                 PTPN11 MUTATED PTPN11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                         6              432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     0   5
  PTPN11 WILD-TYPE  18 415
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      0    5
  PTPN11 WILD-TYPE   18  415
                        clus
vv                       PTPN11 MUTATED PTPN11 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              5              415
[1] 2 2
[1] FALSE

Clustering(31) Variable = GAGE2D MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  GAGE2D MUTATED     4   1
  GAGE2D WILD-TYPE 374  92
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              466 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               1               92 
$`GAGE2D MUTATED`
TCGA-DU-5849 TCGA-DU-A7TJ TCGA-E1-5303 TCGA-FG-A4MY TCGA-HT-7481 
       14.56         0.56        67.46        23.70        95.93 

$`GAGE2D WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       13.38         3.45        18.61        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 
        6.54        24.26         6.38        40.34        75.19       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  GAGE2D MUTATED GAGE2D WILD-TYPE 
            0.56             0.03 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           95.93           211.17 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           23.70            18.61 
[1] "0.6 - 95.9 (23.7)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.6"
D31V2, continuous
D31V3, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     1   4
  GAGE2D WILD-TYPE 206 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      1    4
  GAGE2D WILD-TYPE  206  262
        clus
vv       GAGE2D MUTATED GAGE2D WILD-TYPE
  FEMALE              1              206
  MALE                4              262
[1] 2 2
[1] FALSE
D31V4, continuous
[1] "Remove cluster labels:" "GAGE2D MUTATED"        
clus
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5304 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO       TCGA-E1-A7YV 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963       TCGA-FG-5965 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  GAGE2D MUTATED             2                1                 2
  GAGE2D WILD-TYPE         173              118               177
D31V5, multiclass
                   clus
vv                  GAGE2D MUTATED GAGE2D WILD-TYPE
  ASTROCYTOMA                    2              173
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              2              177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     1   4
  GAGE2D WILD-TYPE  91 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      1    4
  GAGE2D WILD-TYPE   91  377
     clus
vv    GAGE2D MUTATED GAGE2D WILD-TYPE
  NO               1               91
  YES              4              377
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAGE2D MUTATED                                  0     0
  GAGE2D WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAGE2D MUTATED                           1     4
  GAGE2D WILD-TYPE                        14   434
D31V7, multiclass
                                  clus
vv                                 GAGE2D MUTATED GAGE2D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     1               14
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     1   4
  GAGE2D WILD-TYPE  17 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      1    4
  GAGE2D WILD-TYPE   17  416
                        clus
vv                       GAGE2D MUTATED GAGE2D WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(32) Variable = ARID2 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED     9   2
  ARID2 WILD-TYPE 369  91
  ARID2 MUTATED ARID2 WILD-TYPE 
             11             460 
  ARID2 MUTATED ARID2 WILD-TYPE 
              2              91 
$`ARID2 MUTATED`
TCGA-DB-A75M TCGA-DH-A7UR TCGA-DU-5855 TCGA-DU-6392 TCGA-DU-A5TY TCGA-DU-A7TB 
       17.88        54.25         6.81       211.17        12.20        42.31 
TCGA-E1-5303 TCGA-FG-A6IZ TCGA-S9-A7IS TCGA-S9-A89V TCGA-TM-A7CA 
       67.46        15.02         7.92        18.71        34.78 

$`ARID2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        12.10        11.24        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        17.19        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        8.45       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC 
        7.13        21.30        17.98       124.50        77.88        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        99.06        30.05        98.63        31.59        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        49.32        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  ARID2 MUTATED ARID2 WILD-TYPE 
           6.81            0.03 
  ARID2 MUTATED ARID2 WILD-TYPE 
         211.17          182.33 
  ARID2 MUTATED ARID2 WILD-TYPE 
          18.71           18.61 
[1] "6.8 - 211.2 (18.7)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.8"
D32V2, continuous
D32V3, binary
                 cls
clus                0   1
  ARID2 MUTATED     5   6
  ARID2 WILD-TYPE 202 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      5    6
  ARID2 WILD-TYPE  202  260
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             5             202
  MALE               6             260
[1] 2 2
[1] FALSE
D32V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ARID2 MUTATED             7                1                 3
  ARID2 WILD-TYPE         168              118               176
D32V5, multiclass
                   clus
vv                  ARID2 MUTATED ARID2 WILD-TYPE
  ASTROCYTOMA                   7             168
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                 cls
clus                0   1
  ARID2 MUTATED     3   8
  ARID2 WILD-TYPE  89 373
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      3    8
  ARID2 WILD-TYPE   89  373
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              3              89
  YES             8             373
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           0    10
  ARID2 WILD-TYPE                        15   428
D32V7, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               7
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                       10             428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                 cls
clus                0   1
  ARID2 MUTATED     0  11
  ARID2 WILD-TYPE  18 409
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      0   11
  ARID2 WILD-TYPE   18  409
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            11             409
[1] 2 2
[1] FALSE

Clustering(33) Variable = ZMIZ1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  ZMIZ1 MUTATED     8   0
  ZMIZ1 WILD-TYPE 370  93
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              8             463 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              0              93 
$`ZMIZ1 MUTATED`
TCGA-DU-6392 TCGA-DU-7009 TCGA-HT-8564 TCGA-QH-A6CU TCGA-QH-A6X8 TCGA-R8-A6MO 
      211.17       138.28        15.72        14.83        16.73        32.65 
TCGA-RY-A843 TCGA-TQ-A7RH 
        2.07        15.98 

$`ZMIZ1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 
        7.73        11.47        62.96       156.23        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       13.74        28.27         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        19.33        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 
       25.38        18.61        14.93        23.80        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           2.07            0.03 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         211.17          182.33 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         16.355          18.610 
[1] "2.1 - 211.2 (16.4)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.9e+07"
D33V2, continuous
D33V3, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     5   3
  ZMIZ1 WILD-TYPE 202 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      5    3
  ZMIZ1 WILD-TYPE  202  263
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  FEMALE             5             202
  MALE               3             263
[1] 2 2
[1] FALSE
D33V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZMIZ1 MUTATED             3                1                 4
  ZMIZ1 WILD-TYPE         172              118               175
D33V5, multiclass
                   clus
vv                  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             4             175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     1   7
  ZMIZ1 WILD-TYPE  91 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      1    7
  ZMIZ1 WILD-TYPE   91  374
     clus
vv    ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  NO              1              91
  YES             7             374
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMIZ1 MUTATED                                  0     1
  ZMIZ1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ1 MUTATED                           0     6
  ZMIZ1 WILD-TYPE                        15   432
D33V7, multiclass
                                  clus
vv                                 ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               7
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     2   5
  ZMIZ1 WILD-TYPE  16 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      2    5
  ZMIZ1 WILD-TYPE   16  415
                        clus
vv                       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(34) Variable = PDGFRA MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED     4   4
  PDGFRA WILD-TYPE 374  89
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               8              463 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               4               89 
$`PDGFRA MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DU-6392 TCGA-FG-A6J1 TCGA-HT-7469 TCGA-HT-7478 
        7.69        12.43       211.17        16.44        11.54         6.38 
TCGA-HT-7882 TCGA-S9-A7IS 
        3.72         7.92 

$`PDGFRA WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       13.58         5.72        27.52         0.10         6.67        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
            3.72             0.03 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          211.17           182.33 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
            9.73            18.71 
[1] "3.7 - 211.2 (9.7)"  "0.0 - 182.3 (18.7)"
[1] "hr=" "2.3"
D34V2, continuous
D34V3, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     4   4
  PDGFRA WILD-TYPE 203 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      4    4
  PDGFRA WILD-TYPE  203  262
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE              4              203
  MALE                4              262
[1] 2 2
[1] FALSE
D34V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PDGFRA MUTATED             5                0                 3
  PDGFRA WILD-TYPE         170              119               176
D34V5, multiclass
                   clus
vv                  PDGFRA MUTATED PDGFRA WILD-TYPE
  ASTROCYTOMA                    5              170
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     4   4
  PDGFRA WILD-TYPE  88 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      4    4
  PDGFRA WILD-TYPE   88  377
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO               4               88
  YES              4              377
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDGFRA MUTATED                                  0     0
  PDGFRA WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PDGFRA MUTATED                           0     8
  PDGFRA WILD-TYPE                        15   430
D34V7, multiclass
                                  clus
vv                                 PDGFRA MUTATED PDGFRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         8              430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     1   7
  PDGFRA WILD-TYPE  17 413
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      1    7
  PDGFRA WILD-TYPE   17  413
                        clus
vv                       PDGFRA MUTATED PDGFRA WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              7              413
[1] 2 2
[1] FALSE

Clustering(35) Variable = ZNF512B MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  ZNF512B MUTATED     4   0
  ZNF512B WILD-TYPE 374  93
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                4               467 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                0                93 
$`ZNF512B MUTATED`
TCGA-DU-6392 TCGA-HT-7471 TCGA-HT-7688 TCGA-S9-A6U6 
      211.17         0.13        31.69        16.08 

$`ZNF512B WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54        40.11         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  ZNF512B MUTATED ZNF512B WILD-TYPE 
             0.13              0.03 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
           211.17            182.33 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
           23.885            18.610 
[1] "0.1 - 211.2 (23.9)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D35V2, continuous
D35V3, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     2   2
  ZNF512B WILD-TYPE 205 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      2    2
  ZNF512B WILD-TYPE  205  264
        clus
vv       ZNF512B MUTATED ZNF512B WILD-TYPE
  FEMALE               2               205
  MALE                 2               264
[1] 2 2
[1] FALSE
D35V4, continuous
[1] "Remove cluster labels:" "ZNF512B MUTATED"       
clus
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                1               268 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YO 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6        TCGA-FG-5963 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7485 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A61A        TCGA-HT-A61B 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-HT-A61C        TCGA-HT-A74L        TCGA-IK-7675        TCGA-KT-A74X 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-KT-A7W1        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F4 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-P5-A5F6        TCGA-P5-A731        TCGA-QH-A65R        TCGA-QH-A65S 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-QH-A65V        TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-QH-A6CU        TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870        TCGA-RY-A83Y 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-RY-A840        TCGA-RY-A845        TCGA-RY-A847        TCGA-S9-A6TS 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U8        TCGA-S9-A6UA 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
       TCGA-VM-A8CE        TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" "ZNF512B WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZNF512B MUTATED             2                0                 2
  ZNF512B WILD-TYPE         173              119               177
D35V5, multiclass
                   clus
vv                  ZNF512B MUTATED ZNF512B WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                0               119
  OLIGODENDROGLIOMA               2               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     2   2
  ZNF512B WILD-TYPE  90 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      2    2
  ZNF512B WILD-TYPE   90  379
     clus
vv    ZNF512B MUTATED ZNF512B WILD-TYPE
  NO                2                90
  YES               2               379
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF512B MUTATED                                  0     0
  ZNF512B WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF512B MUTATED                           0     4
  ZNF512B WILD-TYPE                        15   434
D35V7, multiclass
                                  clus
vv                                 ZNF512B MUTATED ZNF512B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          4               434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     0   4
  ZNF512B WILD-TYPE  18 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      0    4
  ZNF512B WILD-TYPE   18  416
                        clus
vv                       ZNF512B MUTATED ZNF512B WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               4               416
[1] 2 2
[1] FALSE

Clustering(36) Variable = PPL MUTATION ANALYSIS
D36V1, survival
               sevent
clus2             0   1
  PPL MUTATED     5   0
  PPL WILD-TYPE 373  93
  PPL MUTATED PPL WILD-TYPE 
            5           466 
  PPL MUTATED PPL WILD-TYPE 
            0            93 
$`PPL MUTATED`
TCGA-DH-A66B TCGA-DU-6392 TCGA-HT-A615 TCGA-R8-A6MK TCGA-VM-A8C8 
       42.05       211.17        16.93        88.83        43.04 

$`PPL WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       11.08        12.99        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       23.80        15.98        26.99        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  PPL MUTATED PPL WILD-TYPE 
        16.93          0.03 
  PPL MUTATED PPL WILD-TYPE 
       211.17        182.33 
  PPL MUTATED PPL WILD-TYPE 
        43.04         18.56 
[1] "16.9 - 211.2 (43.0)" "0.0 - 182.3 (18.6)" 
[1] "hr="     "2.7e+07"
D36V2, continuous
D36V3, binary
               cls
clus              0   1
  PPL MUTATED     3   2
  PPL WILD-TYPE 204 264
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      3    2
  PPL WILD-TYPE  204  264
        clus
vv       PPL MUTATED PPL WILD-TYPE
  FEMALE           3           204
  MALE             2           264
[1] 2 2
[1] FALSE
D36V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PPL MUTATED             2                0                 3
  PPL WILD-TYPE         173              119               176
D36V5, multiclass
                   clus
vv                  PPL MUTATED PPL WILD-TYPE
  ASTROCYTOMA                 2           173
  OLIGOASTROCYTOMA            0           119
  OLIGODENDROGLIOMA           3           176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
               cls
clus              0   1
  PPL MUTATED     1   4
  PPL WILD-TYPE  91 377
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      1    4
  PPL WILD-TYPE   91  377
     clus
vv    PPL MUTATED PPL WILD-TYPE
  NO            1            91
  YES           4           377
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPL MUTATED                                  0     0
  PPL WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PPL MUTATED                           0     5
  PPL WILD-TYPE                        15   433
D36V7, multiclass
                                  clus
vv                                 PPL MUTATED PPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                      5           433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
               cls
clus              0   1
  PPL MUTATED     0   4
  PPL WILD-TYPE  18 416
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      0    4
  PPL WILD-TYPE   18  416
                        clus
vv                       PPL MUTATED PPL WILD-TYPE
  HISPANIC OR LATINO               0            18
  NOT HISPANIC OR LATINO           4           416
[1] 2 2
[1] FALSE

Clustering(37) Variable = PRX MUTATION ANALYSIS
D37V1, survival
               sevent
clus2             0   1
  PRX MUTATED     7   3
  PRX WILD-TYPE 371  90
  PRX MUTATED PRX WILD-TYPE 
           10           461 
  PRX MUTATED PRX WILD-TYPE 
            3            90 
$`PRX MUTATED`
TCGA-DU-6392 TCGA-DU-7300 TCGA-FG-A4MW TCGA-HT-8018 TCGA-HT-8564 TCGA-HT-A74H 
      211.17        62.01        18.38        37.87        15.72         2.43 
TCGA-P5-A5EX TCGA-S9-A6U0 TCGA-S9-A7J0 TCGA-S9-A7QX 
        1.64        22.95        20.02        13.12 

$`PRX WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 
        1.64        16.24         9.40        63.55         0.10        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J 
       16.83        21.40         6.38        17.52        17.65        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       42.77        14.40        14.40         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       37.84        34.49        31.33        28.70        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        22.32        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        15.06        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  PRX MUTATED PRX WILD-TYPE 
         1.64          0.03 
  PRX MUTATED PRX WILD-TYPE 
       211.17        182.33 
  PRX MUTATED PRX WILD-TYPE 
        19.20         18.61 
[1] "1.6 - 211.2 (19.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D37V2, continuous
D37V3, binary
               cls
clus              0   1
  PRX MUTATED     6   4
  PRX WILD-TYPE 201 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  PRX MUTATED      6    4
  PRX WILD-TYPE  201  262
        clus
vv       PRX MUTATED PRX WILD-TYPE
  FEMALE           6           201
  MALE             4           262
[1] 2 2
[1] FALSE
D37V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PRX MUTATED             5                2                 3
  PRX WILD-TYPE         170              117               176
D37V5, multiclass
                   clus
vv                  PRX MUTATED PRX WILD-TYPE
  ASTROCYTOMA                 5           170
  OLIGOASTROCYTOMA            2           117
  OLIGODENDROGLIOMA           3           176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
               cls
clus              0   1
  PRX MUTATED     1   9
  PRX WILD-TYPE  91 372
[1] "tbl2"
               cls
clus            [,1] [,2]
  PRX MUTATED      1    9
  PRX WILD-TYPE   91  372
     clus
vv    PRX MUTATED PRX WILD-TYPE
  NO            1            91
  YES           9           372
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRX MUTATED                                  0     0
  PRX WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PRX MUTATED                           0    10
  PRX WILD-TYPE                        15   428
D37V7, multiclass
                                  clus
vv                                 PRX MUTATED PRX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                     10           428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
               cls
clus              0   1
  PRX MUTATED     1   9
  PRX WILD-TYPE  17 411
[1] "tbl2"
               cls
clus            [,1] [,2]
  PRX MUTATED      1    9
  PRX WILD-TYPE   17  411
                        clus
vv                       PRX MUTATED PRX WILD-TYPE
  HISPANIC OR LATINO               1            17
  NOT HISPANIC OR LATINO           9           411
[1] 2 2
[1] FALSE

Clustering(38) Variable = NKD2 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  NKD2 MUTATED     3   1
  NKD2 WILD-TYPE 375  92
  NKD2 MUTATED NKD2 WILD-TYPE 
             4            467 
  NKD2 MUTATED NKD2 WILD-TYPE 
             1             92 
$`NKD2 MUTATED`
TCGA-CS-6668 TCGA-S9-A6TZ TCGA-VW-A8FI TCGA-WY-A85A 
        8.02        28.70         8.05        43.40 

$`NKD2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       37.84        34.49        31.33        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        45.80        46.88        37.71        20.81 

  NKD2 MUTATED NKD2 WILD-TYPE 
          8.02           0.03 
  NKD2 MUTATED NKD2 WILD-TYPE 
         43.40         211.17 
  NKD2 MUTATED NKD2 WILD-TYPE 
        18.375         18.610 
[1] "8.0 - 43.4 (18.4)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.8"
D38V2, continuous
D38V3, binary
                cls
clus               0   1
  NKD2 MUTATED     2   2
  NKD2 WILD-TYPE 205 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      2    2
  NKD2 WILD-TYPE  205  264
        clus
vv       NKD2 MUTATED NKD2 WILD-TYPE
  FEMALE            2            205
  MALE              2            264
[1] 2 2
[1] FALSE
D38V4, continuous
[1] "Remove cluster labels:" "NKD2 MUTATED"          
clus
  NKD2 MUTATED NKD2 WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE     TCGA-DB-A64L 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S     TCGA-DB-A64U 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X     TCGA-DB-A75L 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142     TCGA-DH-5143 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D     TCGA-DH-A66F 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU     TCGA-DH-A7UV 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853     TCGA-DU-5854 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871     TCGA-DU-5874 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404     TCGA-DU-6405 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410     TCGA-DU-7011 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018     TCGA-DU-7019 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299     TCGA-DU-7300 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304     TCGA-DU-7306 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161     TCGA-DU-8162 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167     TCGA-DU-8168 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS     TCGA-DU-A5TU 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6     TCGA-DU-A6S7 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6     TCGA-DU-A7T8 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC     TCGA-DU-A7TD 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311     TCGA-E1-5318 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO     TCGA-E1-A7YV 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963     TCGA-FG-5965 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690     TCGA-FG-6691 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181     TCGA-FG-8185 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3     TCGA-FG-A711 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615     TCGA-HT-A617 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2     TCGA-S9-A6U5 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA     TCGA-S9-A6UB 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG     TCGA-S9-A6WH 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM     TCGA-S9-A6WN 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ     TCGA-S9-A7IQ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NKD2 MUTATED             3                0                 1
  NKD2 WILD-TYPE         172              119               178
D38V5, multiclass
                   clus
vv                  NKD2 MUTATED NKD2 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                cls
clus               0   1
  NKD2 MUTATED     0   4
  NKD2 WILD-TYPE  92 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      0    4
  NKD2 WILD-TYPE   92  377
     clus
vv    NKD2 MUTATED NKD2 WILD-TYPE
  NO             0             92
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NKD2 MUTATED                                  0     0
  NKD2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NKD2 MUTATED                           0     4
  NKD2 WILD-TYPE                        15   434
D38V7, multiclass
                                  clus
vv                                 NKD2 MUTATED NKD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                cls
clus               0   1
  NKD2 MUTATED     0   3
  NKD2 WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      0    3
  NKD2 WILD-TYPE   18  417
                        clus
vv                       NKD2 MUTATED NKD2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(39) Variable = IRS4 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED     6   1
  IRS4 WILD-TYPE 372  92
  IRS4 MUTATED IRS4 WILD-TYPE 
             7            464 
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             92 
$`IRS4 MUTATED`
TCGA-DB-A4XD TCGA-DB-A64L TCGA-DU-6392 TCGA-E1-5304 TCGA-HT-8108 TCGA-HT-8564 
       39.78        24.20       211.17        41.13         2.50        15.72 
TCGA-S9-A6WG 
       80.12 

$`IRS4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        46.72        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.10         0.46         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-A4DS 
        0.23        29.59        34.19        13.74        28.27         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI 
        5.85       106.39        69.50        72.59        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  IRS4 MUTATED IRS4 WILD-TYPE 
          2.50           0.03 
  IRS4 MUTATED IRS4 WILD-TYPE 
        211.17         182.33 
  IRS4 MUTATED IRS4 WILD-TYPE 
         39.78          18.56 
[1] "2.5 - 211.2 (39.8)" "0.0 - 182.3 (18.6)"
[1] "hr=" "3.2"
D39V2, continuous
D39V3, binary
                cls
clus               0   1
  IRS4 MUTATED     3   4
  IRS4 WILD-TYPE 204 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      3    4
  IRS4 WILD-TYPE  204  262
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            3            204
  MALE              4            262
[1] 2 2
[1] FALSE
D39V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IRS4 MUTATED             5                0                 2
  IRS4 WILD-TYPE         170              119               177
D39V5, multiclass
                   clus
vv                  IRS4 MUTATED IRS4 WILD-TYPE
  ASTROCYTOMA                  5            170
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                cls
clus               0   1
  IRS4 MUTATED     2   5
  IRS4 WILD-TYPE  90 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2    5
  IRS4 WILD-TYPE   90  376
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             2             90
  YES            5            376
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRS4 MUTATED                                  0     0
  IRS4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED                           0     7
  IRS4 WILD-TYPE                        15   431
D39V7, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       7            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                cls
clus               0   1
  IRS4 MUTATED     1   6
  IRS4 WILD-TYPE  17 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1    6
  IRS4 WILD-TYPE   17  414
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            6            414
[1] 2 2
[1] FALSE

Clustering(40) Variable = SPTAN1 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  SPTAN1 MUTATED     5   0
  SPTAN1 WILD-TYPE 373  93
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               5              466 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               0               93 
$`SPTAN1 MUTATED`
TCGA-DH-5142 TCGA-DU-6392 TCGA-HT-7875 TCGA-HT-8564 TCGA-S9-A7R3 
       30.31       211.17         0.33        15.72        99.06 

$`SPTAN1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 
        0.23        50.63         0.49        23.61        37.15         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
            0.33             0.03 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
          211.17           182.33 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
           30.31            18.61 
[1] "0.3 - 211.2 (30.3)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D40V2, continuous
D40V3, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     2   3
  SPTAN1 WILD-TYPE 205 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      2    3
  SPTAN1 WILD-TYPE  205  263
        clus
vv       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  FEMALE              2              205
  MALE                3              263
[1] 2 2
[1] FALSE
D40V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SPTAN1 MUTATED             4                0                 1
  SPTAN1 WILD-TYPE         171              119               178
D40V5, multiclass
                   clus
vv                  SPTAN1 MUTATED SPTAN1 WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     2   3
  SPTAN1 WILD-TYPE  90 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      2    3
  SPTAN1 WILD-TYPE   90  378
     clus
vv    SPTAN1 MUTATED SPTAN1 WILD-TYPE
  NO               2               90
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPTAN1 MUTATED                                  0     0
  SPTAN1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPTAN1 MUTATED                           0     5
  SPTAN1 WILD-TYPE                        15   433
D40V7, multiclass
                                  clus
vv                                 SPTAN1 MUTATED SPTAN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         5              433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     1   4
  SPTAN1 WILD-TYPE  17 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      1    4
  SPTAN1 WILD-TYPE   17  416
                        clus
vv                       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(41) Variable = CIB1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  CIB1 MUTATED     4   0
  CIB1 WILD-TYPE 374  93
  CIB1 MUTATED CIB1 WILD-TYPE 
             4            467 
  CIB1 MUTATED CIB1 WILD-TYPE 
             0             93 
$`CIB1 MUTATED`
TCGA-HT-7477 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-TM-A7C5 
       24.26        20.22         0.07        49.32 

$`CIB1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.13        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        48.33        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  CIB1 MUTATED CIB1 WILD-TYPE 
          0.07           0.03 
  CIB1 MUTATED CIB1 WILD-TYPE 
         49.32         211.17 
  CIB1 MUTATED CIB1 WILD-TYPE 
         22.24          18.61 
[1] "0.1 - 49.3 (22.2)"  "0.0 - 211.2 (18.6)"
[1] "hr="     "3300000"
D41V2, continuous
D41V3, binary
                cls
clus               0   1
  CIB1 MUTATED     2   2
  CIB1 WILD-TYPE 205 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB1 MUTATED      2    2
  CIB1 WILD-TYPE  205  264
        clus
vv       CIB1 MUTATED CIB1 WILD-TYPE
  FEMALE            2            205
  MALE              2            264
[1] 2 2
[1] FALSE
D41V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CIB1 MUTATED             2                1                 1
  CIB1 WILD-TYPE         173              118               178
D41V5, multiclass
                   clus
vv                  CIB1 MUTATED CIB1 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             1            118
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                cls
clus               0   1
  CIB1 MUTATED     0   4
  CIB1 WILD-TYPE  92 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB1 MUTATED      0    4
  CIB1 WILD-TYPE   92  377
     clus
vv    CIB1 MUTATED CIB1 WILD-TYPE
  NO             0             92
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIB1 MUTATED                                  0     0
  CIB1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CIB1 MUTATED                           0     4
  CIB1 WILD-TYPE                        15   434
D41V7, multiclass
                                  clus
vv                                 CIB1 MUTATED CIB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                cls
clus               0   1
  CIB1 MUTATED     0   4
  CIB1 WILD-TYPE  18 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB1 MUTATED      0    4
  CIB1 WILD-TYPE   18  416
                        clus
vv                       CIB1 MUTATED CIB1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE

Clustering(42) Variable = EIF1AX MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  EIF1AX MUTATED     4   0
  EIF1AX WILD-TYPE 374  93
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              467 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               0               93 
$`EIF1AX MUTATED`
TCGA-DB-A4XB TCGA-DU-7306 TCGA-DU-A5TP TCGA-HT-7609 
       30.21        41.98        14.24        45.99 

$`EIF1AX WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        23.31         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
           14.24             0.03 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           45.99           211.17 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          36.095           18.610 
[1] "14.2 - 46.0 (36.1)" "0.0 - 211.2 (18.6)"
[1] "hr="     "9100000"
D42V2, continuous
D42V3, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   4
  EIF1AX WILD-TYPE 207 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    4
  EIF1AX WILD-TYPE  207  262
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              0              207
  MALE                4              262
[1] 2 2
[1] FALSE
D42V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EIF1AX MUTATED             2                2                 0
  EIF1AX WILD-TYPE         173              117               179
D42V5, multiclass
                   clus
vv                  EIF1AX MUTATED EIF1AX WILD-TYPE
  ASTROCYTOMA                    2              173
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              0              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     2   2
  EIF1AX WILD-TYPE  90 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      2    2
  EIF1AX WILD-TYPE   90  379
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               2               90
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF1AX MUTATED                                  0     0
  EIF1AX WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF1AX MUTATED                           0     4
  EIF1AX WILD-TYPE                        15   434
D42V7, multiclass
                                  clus
vv                                 EIF1AX MUTATED EIF1AX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   4
  EIF1AX WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    4
  EIF1AX WILD-TYPE   18  416
                        clus
vv                       EIF1AX MUTATED EIF1AX WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(43) Variable = SCN4A MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  SCN4A MUTATED     5   1
  SCN4A WILD-TYPE 373  92
  SCN4A MUTATED SCN4A WILD-TYPE 
              6             465 
  SCN4A MUTATED SCN4A WILD-TYPE 
              1              92 
$`SCN4A MUTATED`
TCGA-DB-5274 TCGA-DU-6392 TCGA-DU-A7TG TCGA-HT-7695 TCGA-P5-A5F2 TCGA-S9-A7QZ 
       75.25       211.17        44.42        14.53         7.63        13.02 

$`SCN4A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TJ 
      124.50        77.88        42.31        23.51         7.50         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
        6.90        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       13.12        28.37       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  SCN4A MUTATED SCN4A WILD-TYPE 
           7.63            0.03 
  SCN4A MUTATED SCN4A WILD-TYPE 
         211.17          182.33 
  SCN4A MUTATED SCN4A WILD-TYPE 
         29.475          18.610 
[1] "7.6 - 211.2 (29.5)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.8"
D43V2, continuous
D43V3, binary
                 cls
clus                0   1
  SCN4A MUTATED     4   2
  SCN4A WILD-TYPE 203 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED      4    2
  SCN4A WILD-TYPE  203  264
        clus
vv       SCN4A MUTATED SCN4A WILD-TYPE
  FEMALE             4             203
  MALE               2             264
[1] 2 2
[1] FALSE
D43V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SCN4A MUTATED             2                1                 3
  SCN4A WILD-TYPE         173              118               176
D43V5, multiclass
                   clus
vv                  SCN4A MUTATED SCN4A WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                 cls
clus                0   1
  SCN4A MUTATED     3   3
  SCN4A WILD-TYPE  89 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED      3    3
  SCN4A WILD-TYPE   89  378
     clus
vv    SCN4A MUTATED SCN4A WILD-TYPE
  NO              3              89
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN4A MUTATED                                  0     0
  SCN4A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN4A MUTATED                           0     6
  SCN4A WILD-TYPE                        15   432
D43V7, multiclass
                                  clus
vv                                 SCN4A MUTATED SCN4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                 cls
clus                0   1
  SCN4A MUTATED     0   6
  SCN4A WILD-TYPE  18 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED      0    6
  SCN4A WILD-TYPE   18  414
                        clus
vv                       SCN4A MUTATED SCN4A WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             414
[1] 2 2
[1] FALSE

Clustering(44) Variable = PLCG1 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  PLCG1 MUTATED     2   4
  PLCG1 WILD-TYPE 376  89
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              6             465 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4              89 
$`PLCG1 MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-8161 TCGA-QH-A6CU 
        7.69        21.01         6.74         6.81        23.74        14.83 

$`PLCG1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 
       18.61        18.02        14.56        17.46        13.38         8.45 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76         5.10        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       15.85        14.04        19.33        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  PLCG1 MUTATED PLCG1 WILD-TYPE 
           6.74            0.03 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
          23.74          211.17 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
          11.26           18.61 
[1] "6.7 - 23.7 (11.3)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "10" 
D44V2, continuous
D44V3, binary
                 cls
clus                0   1
  PLCG1 MUTATED     4   2
  PLCG1 WILD-TYPE 203 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      4    2
  PLCG1 WILD-TYPE  203  264
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  FEMALE             4             203
  MALE               2             264
[1] 2 2
[1] FALSE
D44V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PLCG1 MUTATED             1                3                 2
  PLCG1 WILD-TYPE         174              116               177
D44V5, multiclass
                   clus
vv                  PLCG1 MUTATED PLCG1 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                 cls
clus                0   1
  PLCG1 MUTATED     2   4
  PLCG1 WILD-TYPE  90 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      2    4
  PLCG1 WILD-TYPE   90  377
     clus
vv    PLCG1 MUTATED PLCG1 WILD-TYPE
  NO              2              90
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCG1 MUTATED                                  0     0
  PLCG1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCG1 MUTATED                           1     5
  PLCG1 WILD-TYPE                        14   433
D44V7, multiclass
                                  clus
vv                                 PLCG1 MUTATED PLCG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    1              14
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                 cls
clus                0   1
  PLCG1 MUTATED     0   5
  PLCG1 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      0    5
  PLCG1 WILD-TYPE   18  415
                        clus
vv                       PLCG1 MUTATED PLCG1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(45) Variable = DLC1 MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   2
  DLC1 WILD-TYPE 375  91
  DLC1 MUTATED DLC1 WILD-TYPE 
             5            466 
  DLC1 MUTATED DLC1 WILD-TYPE 
             2             91 
$`DLC1 MUTATED`
TCGA-DU-6392 TCGA-DU-6395 TCGA-FG-7638 TCGA-HT-8011 TCGA-HT-A5RC 
      211.17        49.02        22.55        16.24         5.33 

$`DLC1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        40.08        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  DLC1 MUTATED DLC1 WILD-TYPE 
          5.33           0.03 
  DLC1 MUTATED DLC1 WILD-TYPE 
        211.17         182.33 
  DLC1 MUTATED DLC1 WILD-TYPE 
         22.55          18.61 
[1] "5.3 - 211.2 (22.6)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D45V2, continuous
D45V3, binary
                cls
clus               0   1
  DLC1 MUTATED     3   2
  DLC1 WILD-TYPE 204 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    2
  DLC1 WILD-TYPE  204  264
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  FEMALE            3            204
  MALE              2            264
[1] 2 2
[1] FALSE
D45V4, continuous
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-8168     TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-A5TU     TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-A6S7     TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-A7T8     TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DU-A7TD     TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E1-5304     TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E1-A7YV     TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-5965     TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-6691     TCGA-FG-7636     TCGA-FG-8181     TCGA-FG-8185 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3     TCGA-FG-A711 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-A5RA     TCGA-HT-A615     TCGA-HT-A617     TCGA-HT-A618 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C     TCGA-HT-A74L 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1     TCGA-P5-A5EU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX     TCGA-P5-A5F0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6     TCGA-P5-A731 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V     TCGA-QH-A65X 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU     TCGA-QH-A6CV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY     TCGA-QH-A6CZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5     TCGA-QH-A6X8 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC     TCGA-QH-A86X 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840     TCGA-RY-A845 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU     TCGA-S9-A6TV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY     TCGA-S9-A6TZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2     TCGA-S9-A6U5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA     TCGA-S9-A6UB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG     TCGA-S9-A6WH 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM     TCGA-S9-A6WN 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ     TCGA-S9-A7IQ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DLC1 MUTATED             3                1                 1
  DLC1 WILD-TYPE         172              118               178
D45V5, multiclass
                   clus
vv                  DLC1 MUTATED DLC1 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             1            118
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                cls
clus               0   1
  DLC1 MUTATED     3   2
  DLC1 WILD-TYPE  89 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    2
  DLC1 WILD-TYPE   89  379
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             3             89
  YES            2            379
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLC1 MUTATED                                  0     0
  DLC1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED                           0     5
  DLC1 WILD-TYPE                        15   433
D45V7, multiclass
                                  clus
vv                                 DLC1 MUTATED DLC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                cls
clus               0   1
  DLC1 MUTATED     0   5
  DLC1 WILD-TYPE  18 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      0    5
  DLC1 WILD-TYPE   18  415
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            415
[1] 2 2
[1] FALSE

Clustering(46) Variable = TMEM216 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     3   0
  TMEM216 WILD-TYPE 375  93
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               468 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                0                93 
$`TMEM216 MUTATED`
TCGA-FG-A60J TCGA-HT-A5R9 TCGA-P5-A5F4 
       14.76         0.07         0.76 

$`TMEM216 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K 
       38.27        10.72        18.38        18.71        23.70        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  TMEM216 MUTATED TMEM216 WILD-TYPE 
             0.07              0.03 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
            14.76            211.17 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
             0.76             18.66 
[1] "0.1 - 14.8 (0.8)"   "0.0 - 211.2 (18.7)"
[1] "hr="    "440000"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     3   0
  TMEM216 WILD-TYPE 204 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      3    0
  TMEM216 WILD-TYPE  204  266
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  FEMALE               3               204
  MALE                 0               266
[1] 2 2
[1] FALSE
D46V4, continuous
[1] "Remove cluster labels:" "TMEM216 MUTATED"       
clus
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                2               267 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YO 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6        TCGA-FG-5963 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3        TCGA-FG-A711 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468        TCGA-HT-7470 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7485        TCGA-HT-7607 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689        TCGA-HT-7692 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7875 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R7 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-A618        TCGA-HT-A61A        TCGA-HT-A61B        TCGA-HT-A61C 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-A74L        TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F6        TCGA-P5-A731 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A870        TCGA-RY-A83Y        TCGA-RY-A840        TCGA-RY-A845 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-RY-A847        TCGA-S9-A6TS        TCGA-S9-A6TU        TCGA-S9-A6TV 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6TW        TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6U6        TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T        TCGA-TQ-A7RW 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TMEM216 MUTATED             0                1                 2
  TMEM216 WILD-TYPE         175              118               177
D46V5, multiclass
                   clus
vv                  TMEM216 MUTATED TMEM216 WILD-TYPE
  ASTROCYTOMA                     0               175
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               2               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   3
  TMEM216 WILD-TYPE  92 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    3
  TMEM216 WILD-TYPE   92  378
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                0                92
  YES               3               378
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM216 MUTATED                                  0     0
  TMEM216 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM216 MUTATED                           0     3
  TMEM216 WILD-TYPE                        15   435
D46V7, multiclass
                                  clus
vv                                 TMEM216 MUTATED TMEM216 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   3
  TMEM216 WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    3
  TMEM216 WILD-TYPE   18  417
                        clus
vv                       TMEM216 MUTATED TMEM216 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               417
[1] 2 2
[1] FALSE

Clustering(47) Variable = MYT1 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2              0   1
  MYT1 MUTATED     4   2
  MYT1 WILD-TYPE 374  91
  MYT1 MUTATED MYT1 WILD-TYPE 
             6            465 
  MYT1 MUTATED MYT1 WILD-TYPE 
             2             91 
$`MYT1 MUTATED`
TCGA-DU-6392 TCGA-DU-7299 TCGA-HT-8018 TCGA-S9-A7R7 TCGA-TM-A84F TCGA-TM-A84H 
      211.17        44.02        37.87        98.63        59.05        30.44 

$`MYT1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       10.39        99.06        30.05        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       16.18        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  MYT1 MUTATED MYT1 WILD-TYPE 
         30.44           0.03 
  MYT1 MUTATED MYT1 WILD-TYPE 
        211.17         182.33 
  MYT1 MUTATED MYT1 WILD-TYPE 
        51.535         18.440 
[1] "30.4 - 211.2 (51.5)" "0.0 - 182.3 (18.4)" 
[1] "hr=" "1.9"
D47V2, continuous
D47V3, binary
                cls
clus               0   1
  MYT1 MUTATED     3   3
  MYT1 WILD-TYPE 204 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYT1 MUTATED      3    3
  MYT1 WILD-TYPE  204  263
        clus
vv       MYT1 MUTATED MYT1 WILD-TYPE
  FEMALE            3            204
  MALE              3            263
[1] 2 2
[1] FALSE
D47V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MYT1 MUTATED             4                2                 0
  MYT1 WILD-TYPE         171              117               179
D47V5, multiclass
                   clus
vv                  MYT1 MUTATED MYT1 WILD-TYPE
  ASTROCYTOMA                  4            171
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                cls
clus               0   1
  MYT1 MUTATED     2   4
  MYT1 WILD-TYPE  90 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYT1 MUTATED      2    4
  MYT1 WILD-TYPE   90  377
     clus
vv    MYT1 MUTATED MYT1 WILD-TYPE
  NO             2             90
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYT1 MUTATED                                  0     0
  MYT1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYT1 MUTATED                           0     6
  MYT1 WILD-TYPE                        15   432
D47V7, multiclass
                                  clus
vv                                 MYT1 MUTATED MYT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       6            432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                cls
clus               0   1
  MYT1 MUTATED     0   6
  MYT1 WILD-TYPE  18 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYT1 MUTATED      0    6
  MYT1 WILD-TYPE   18  414
                        clus
vv                       MYT1 MUTATED MYT1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            6            414
[1] 2 2
[1] FALSE

Clustering(48) Variable = SMARCB1 MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     3   1
  SMARCB1 WILD-TYPE 375  92
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               467 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                1                92 
$`SMARCB1 MUTATED`
TCGA-DU-6392 TCGA-DU-7019 TCGA-DU-7299 TCGA-HT-7875 
      211.17        26.30        44.02         0.33 

$`SMARCB1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 
      105.21         6.54         8.84        90.77        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        7.96        94.32        18.94        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        23.61        37.15         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
             0.33              0.03 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           211.17            182.33 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            35.16             18.61 
[1] "0.3 - 211.2 (35.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.2"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     1   3
  SMARCB1 WILD-TYPE 206 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      1    3
  SMARCB1 WILD-TYPE  206  263
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               1               206
  MALE                 3               263
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SMARCB1 MUTATED             2                1                 1
  SMARCB1 WILD-TYPE         173              118               178
D48V5, multiclass
                   clus
vv                  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               1               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     3   1
  SMARCB1 WILD-TYPE  89 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      3    1
  SMARCB1 WILD-TYPE   89  380
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO                3                89
  YES               1               380
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           0     4
  SMARCB1 WILD-TYPE                        15   434
D48V7, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          4               434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0   4
  SMARCB1 WILD-TYPE  18 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    4
  SMARCB1 WILD-TYPE   18  416
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               4               416
[1] 2 2
[1] FALSE

Clustering(49) Variable = RIPK4 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  RIPK4 MUTATED     6   2
  RIPK4 WILD-TYPE 372  91
  RIPK4 MUTATED RIPK4 WILD-TYPE 
              8             463 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
              2              91 
$`RIPK4 MUTATED`
TCGA-CS-6188 TCGA-DU-6392 TCGA-F6-A8O3 TCGA-FG-8187 TCGA-FG-A70Z TCGA-HT-8104 
       23.84       211.17         0.23        20.09        10.78        12.23 
TCGA-S9-A7R2 TCGA-TM-A84O 
       10.39        33.24 

$`RIPK4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       36.82        32.35        14.33         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       20.09        12.95        13.68        14.24        16.01        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       22.26        28.54        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        9.40        63.55         0.10        37.87        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84Q 
       30.44        28.08        24.16        40.83        24.79        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  RIPK4 MUTATED RIPK4 WILD-TYPE 
           0.23            0.03 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
         211.17          182.33 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
          16.16           18.61 
[1] "0.2 - 211.2 (16.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.2"
D49V2, continuous
D49V3, binary
                 cls
clus                0   1
  RIPK4 MUTATED     4   4
  RIPK4 WILD-TYPE 203 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      4    4
  RIPK4 WILD-TYPE  203  262
        clus
vv       RIPK4 MUTATED RIPK4 WILD-TYPE
  FEMALE             4             203
  MALE               4             262
[1] 2 2
[1] FALSE
D49V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RIPK4 MUTATED             4                2                 2
  RIPK4 WILD-TYPE         171              117               177
D49V5, multiclass
                   clus
vv                  RIPK4 MUTATED RIPK4 WILD-TYPE
  ASTROCYTOMA                   4             171
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                 cls
clus                0   1
  RIPK4 MUTATED     2   6
  RIPK4 WILD-TYPE  90 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      2    6
  RIPK4 WILD-TYPE   90  375
     clus
vv    RIPK4 MUTATED RIPK4 WILD-TYPE
  NO              2              90
  YES             6             375
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIPK4 MUTATED                                  0     1
  RIPK4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RIPK4 MUTATED                           1     6
  RIPK4 WILD-TYPE                        14   432
D49V7, multiclass
                                  clus
vv                                 RIPK4 MUTATED RIPK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               7
  BLACK OR AFRICAN AMERICAN                    1              14
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                 cls
clus                0   1
  RIPK4 MUTATED     0   8
  RIPK4 WILD-TYPE  18 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      0    8
  RIPK4 WILD-TYPE   18  412
                        clus
vv                       RIPK4 MUTATED RIPK4 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             8             412
[1] 2 2
[1] FALSE

Clustering(50) Variable = NEU2 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  NEU2 MUTATED     3   1
  NEU2 WILD-TYPE 375  92
  NEU2 MUTATED NEU2 WILD-TYPE 
             4            467 
  NEU2 MUTATED NEU2 WILD-TYPE 
             1             92 
$`NEU2 MUTATED`
TCGA-DU-6399 TCGA-HT-A74H TCGA-HW-8322 TCGA-P5-A733 
       65.75         2.43        17.82        13.61 

$`NEU2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
        6.38        17.52        17.65        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31        21.70        21.60        19.59        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S 
       13.25        11.64         0.20         9.01        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  NEU2 MUTATED NEU2 WILD-TYPE 
          2.43           0.03 
  NEU2 MUTATED NEU2 WILD-TYPE 
         65.75         211.17 
  NEU2 MUTATED NEU2 WILD-TYPE 
        15.715         18.610 
[1] "2.4 - 65.8 (15.7)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.4"
D50V2, continuous
D50V3, binary
                cls
clus               0   1
  NEU2 MUTATED     1   3
  NEU2 WILD-TYPE 206 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEU2 MUTATED      1    3
  NEU2 WILD-TYPE  206  263
        clus
vv       NEU2 MUTATED NEU2 WILD-TYPE
  FEMALE            1            206
  MALE              3            263
[1] 2 2
[1] FALSE
D50V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NEU2 MUTATED             2                0                 2
  NEU2 WILD-TYPE         173              119               177
D50V5, multiclass
                   clus
vv                  NEU2 MUTATED NEU2 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                cls
clus               0   1
  NEU2 MUTATED     1   3
  NEU2 WILD-TYPE  91 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEU2 MUTATED      1    3
  NEU2 WILD-TYPE   91  378
     clus
vv    NEU2 MUTATED NEU2 WILD-TYPE
  NO             1             91
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEU2 MUTATED                                  0     0
  NEU2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEU2 MUTATED                           0     4
  NEU2 WILD-TYPE                        15   434
D50V7, multiclass
                                  clus
vv                                 NEU2 MUTATED NEU2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                cls
clus               0   1
  NEU2 MUTATED     0   4
  NEU2 WILD-TYPE  18 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEU2 MUTATED      0    4
  NEU2 WILD-TYPE   18  416
                        clus
vv                       NEU2 MUTATED NEU2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE

Clustering(51) Variable = PTPRH MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  PTPRH MUTATED     6   2
  PTPRH WILD-TYPE 372  91
  PTPRH MUTATED PTPRH WILD-TYPE 
              8             463 
  PTPRH MUTATED PTPRH WILD-TYPE 
              2              91 
$`PTPRH MUTATED`
TCGA-DU-5852 TCGA-DU-6392 TCGA-DU-7010 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-HT-7467 
        6.74       211.17        14.99        17.88        22.26         0.10 
TCGA-HT-7688 TCGA-S9-A89Z 
       31.69        11.97 

$`PTPRH WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72        27.52         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  PTPRH MUTATED PTPRH WILD-TYPE 
           0.10            0.03 
  PTPRH MUTATED PTPRH WILD-TYPE 
         211.17          182.33 
  PTPRH MUTATED PTPRH WILD-TYPE 
         16.435          18.610 
[1] "0.1 - 211.2 (16.4)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D51V2, continuous
D51V3, binary
                 cls
clus                0   1
  PTPRH MUTATED     4   4
  PTPRH WILD-TYPE 203 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED      4    4
  PTPRH WILD-TYPE  203  262
        clus
vv       PTPRH MUTATED PTPRH WILD-TYPE
  FEMALE             4             203
  MALE               4             262
[1] 2 2
[1] FALSE
D51V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PTPRH MUTATED             5                1                 2
  PTPRH WILD-TYPE         170              118               177
D51V5, multiclass
                   clus
vv                  PTPRH MUTATED PTPRH WILD-TYPE
  ASTROCYTOMA                   5             170
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                 cls
clus                0   1
  PTPRH MUTATED     3   5
  PTPRH WILD-TYPE  89 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED      3    5
  PTPRH WILD-TYPE   89  376
     clus
vv    PTPRH MUTATED PTPRH WILD-TYPE
  NO              3              89
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRH MUTATED                                  0     0
  PTPRH WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRH MUTATED                           0     8
  PTPRH WILD-TYPE                        15   430
D51V7, multiclass
                                  clus
vv                                 PTPRH MUTATED PTPRH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        8             430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                 cls
clus                0   1
  PTPRH MUTATED     0   8
  PTPRH WILD-TYPE  18 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED      0    8
  PTPRH WILD-TYPE   18  412
                        clus
vv                       PTPRH MUTATED PTPRH WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             8             412
[1] 2 2
[1] FALSE

Clustering(52) Variable = MAPK15 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  MAPK15 MUTATED     1   2
  MAPK15 WILD-TYPE 377  91
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               3              468 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               2               91 
$`MAPK15 MUTATED`
TCGA-DU-6394 TCGA-DU-A5TT TCGA-S9-A7R8 
       22.42         4.96        31.59 

$`MAPK15 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16       211.17        52.11        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
      169.84        10.39        99.06        30.05        98.63        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  MAPK15 MUTATED MAPK15 WILD-TYPE 
            4.96             0.03 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
           31.59           211.17 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
           22.42            18.61 
[1] "5.0 - 31.6 (22.4)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "5.8"
D52V2, continuous
D52V3, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     1   3
  MAPK15 WILD-TYPE 206 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      1    3
  MAPK15 WILD-TYPE  206  263
        clus
vv       MAPK15 MUTATED MAPK15 WILD-TYPE
  FEMALE              1              206
  MALE                3              263
[1] 2 2
[1] FALSE
D52V4, continuous
[1] "Remove cluster labels:" "MAPK15 MUTATED"        
clus
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-HT-A61C       TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-KT-A7W1       TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-P5-A5EX       TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-P5-A5F6       TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-QH-A65V       TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-QH-A6CU       TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-QH-A6CY       TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-QH-A6X5       TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-QH-A6XC       TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-RY-A840       TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6TU       TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6TY       TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6U2       TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6UA       TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6WG       TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6WM       TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A6WQ       TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A7IY       TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A7J2       TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A7QY       TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A7R3       TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A89V 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" "MAPK15 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MAPK15 MUTATED             1                0                 3
  MAPK15 WILD-TYPE         174              119               176
D52V5, multiclass
                   clus
vv                  MAPK15 MUTATED MAPK15 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     1   3
  MAPK15 WILD-TYPE  91 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      1    3
  MAPK15 WILD-TYPE   91  378
     clus
vv    MAPK15 MUTATED MAPK15 WILD-TYPE
  NO               1               91
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK15 MUTATED                                  0     0
  MAPK15 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAPK15 MUTATED                           0     4
  MAPK15 WILD-TYPE                        15   434
D52V7, multiclass
                                  clus
vv                                 MAPK15 MUTATED MAPK15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     0   4
  MAPK15 WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      0    4
  MAPK15 WILD-TYPE   18  416
                        clus
vv                       MAPK15 MUTATED MAPK15 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(53) Variable = TPX2 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  TPX2 MUTATED     3   0
  TPX2 WILD-TYPE 375  93
  TPX2 MUTATED TPX2 WILD-TYPE 
             3            468 
  TPX2 MUTATED TPX2 WILD-TYPE 
             0             93 
$`TPX2 MUTATED`
TCGA-DU-6392 TCGA-HT-7688 TCGA-S9-A6WL 
      211.17        31.69        31.10 

$`TPX2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM 
       69.50        72.59        80.12        32.45        84.99        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  TPX2 MUTATED TPX2 WILD-TYPE 
         31.10           0.03 
  TPX2 MUTATED TPX2 WILD-TYPE 
        211.17         182.33 
  TPX2 MUTATED TPX2 WILD-TYPE 
         31.69          18.56 
[1] "31.1 - 211.2 (31.7)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D53V2, continuous
D53V3, binary
                cls
clus               0   1
  TPX2 MUTATED     1   2
  TPX2 WILD-TYPE 206 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      1    2
  TPX2 WILD-TYPE  206  264
        clus
vv       TPX2 MUTATED TPX2 WILD-TYPE
  FEMALE            1            206
  MALE              2            264
[1] 2 2
[1] FALSE
D53V4, continuous
[1] "Remove cluster labels:" "TPX2 MUTATED"          
clus
  TPX2 MUTATED TPX2 WILD-TYPE 
             1            268 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-8168     TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-A5TU     TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-A6S7     TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-A7T8     TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-DU-A7TD     TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-E1-5304     TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-E1-A7YV     TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-5965     TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-6691     TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-8185     TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-8189     TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-A60J     TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-FG-A711     TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-7470     TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-7607     TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-7692     TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-7875     TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-A5R7     TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-A617     TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-HT-A61C     TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-KT-A7W1     TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-P5-A5EX     TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-P5-A5F6     TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-QH-A65V     TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-QH-A6CU     TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-QH-A6CY     TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-QH-A6X5     TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-QH-A6XC     TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-RY-A840     TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6TU     TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6TY     TCGA-S9-A6TZ     TCGA-S9-A6U0     TCGA-S9-A6U1 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6U2     TCGA-S9-A6U5     TCGA-S9-A6U6     TCGA-S9-A6U8 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6UA     TCGA-S9-A6UB     TCGA-S9-A6WD     TCGA-S9-A6WE 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6WG     TCGA-S9-A6WH     TCGA-S9-A6WI     TCGA-S9-A6WM 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A6WN     TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A7IQ     TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A7IZ     TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A7J3     TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A7QZ     TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A7R4     TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-S9-A89Z     TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-TM-A7CA     TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-TM-A84F     TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-TM-A84J     TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-TM-A84Q     TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-TQ-A7RW     TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
    TCGA-VM-A8CE     TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" "TPX2 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TPX2 MUTATED             2                0                 1
  TPX2 WILD-TYPE         173              119               178
D53V5, multiclass
                   clus
vv                  TPX2 MUTATED TPX2 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                cls
clus               0   1
  TPX2 MUTATED     2   1
  TPX2 WILD-TYPE  90 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      2    1
  TPX2 WILD-TYPE   90  380
     clus
vv    TPX2 MUTATED TPX2 WILD-TYPE
  NO             2             90
  YES            1            380
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPX2 MUTATED                                  0     0
  TPX2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPX2 MUTATED                           0     3
  TPX2 WILD-TYPE                        15   435
D53V7, multiclass
                                  clus
vv                                 TPX2 MUTATED TPX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                cls
clus               0   1
  TPX2 MUTATED     0   3
  TPX2 WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      0    3
  TPX2 WILD-TYPE   18  417
                        clus
vv                       TPX2 MUTATED TPX2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(54) Variable = SLC12A7 MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  SLC12A7 MUTATED     5   0
  SLC12A7 WILD-TYPE 373  93
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                5               466 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                0                93 
$`SLC12A7 MUTATED`
TCGA-CS-5390 TCGA-DU-5872 TCGA-DU-6392 TCGA-P5-A5EV TCGA-TM-A7C5 
       64.64        17.49       211.17         0.23        49.32 

$`SLC12A7 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        18.94        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
             0.23              0.03 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
           211.17            182.33 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
            49.32             18.61 
[1] "0.2 - 211.2 (49.3)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     3   2
  SLC12A7 WILD-TYPE 204 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      3    2
  SLC12A7 WILD-TYPE  204  264
        clus
vv       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  FEMALE               3               204
  MALE                 2               264
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SLC12A7 MUTATED             2                2                 1
  SLC12A7 WILD-TYPE         173              117               178
D54V5, multiclass
                   clus
vv                  SLC12A7 MUTATED SLC12A7 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                2               117
  OLIGODENDROGLIOMA               1               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     3   2
  SLC12A7 WILD-TYPE  89 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      3    2
  SLC12A7 WILD-TYPE   89  379
     clus
vv    SLC12A7 MUTATED SLC12A7 WILD-TYPE
  NO                3                89
  YES               2               379
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC12A7 MUTATED                                  0     0
  SLC12A7 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC12A7 MUTATED                           1     4
  SLC12A7 WILD-TYPE                        14   434
D54V7, multiclass
                                  clus
vv                                 SLC12A7 MUTATED SLC12A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          4               434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     0   4
  SLC12A7 WILD-TYPE  18 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      0    4
  SLC12A7 WILD-TYPE   18  416
                        clus
vv                       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               4               416
[1] 2 2
[1] FALSE

Clustering(55) Variable = PLXNA3 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  PLXNA3 MUTATED     8   0
  PLXNA3 WILD-TYPE 370  93
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               8              463 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               0               93 
$`PLXNA3 MUTATED`
TCGA-CS-5396 TCGA-DU-5872 TCGA-DU-6392 TCGA-FG-6688 TCGA-FG-8185 TCGA-FG-A4MU 
        9.96        17.49       211.17        18.77        14.24        10.72 
TCGA-HT-A615 TCGA-QH-A6CU 
       16.93        14.83 

$`PLXNA3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        18.94        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       34.36        36.82        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       32.61        38.27        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        5.33         2.70         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
            9.96             0.03 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
          211.17           182.33 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
           15.88            18.71 
[1] "10.0 - 211.2 (15.9)" "0.0 - 182.3 (18.7)" 
[1] "hr="   "1e+07"
D55V2, continuous
D55V3, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED     6   2
  PLXNA3 WILD-TYPE 201 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      6    2
  PLXNA3 WILD-TYPE  201  264
        clus
vv       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  FEMALE              6              201
  MALE                2              264
[1] 2 2
[1] FALSE
D55V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PLXNA3 MUTATED             3                2                 3
  PLXNA3 WILD-TYPE         172              117               176
D55V5, multiclass
                   clus
vv                  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  ASTROCYTOMA                    3              172
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED     4   4
  PLXNA3 WILD-TYPE  88 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      4    4
  PLXNA3 WILD-TYPE   88  377
     clus
vv    PLXNA3 MUTATED PLXNA3 WILD-TYPE
  NO               4               88
  YES              4              377
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLXNA3 MUTATED                                  0     0
  PLXNA3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLXNA3 MUTATED                           2     6
  PLXNA3 WILD-TYPE                        13   432
D55V7, multiclass
                                  clus
vv                                 PLXNA3 MUTATED PLXNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     2               13
  WHITE                                         6              432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED     0   8
  PLXNA3 WILD-TYPE  18 412
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      0    8
  PLXNA3 WILD-TYPE   18  412
                        clus
vv                       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              8              412
[1] 2 2
[1] FALSE

Clustering(56) Variable = RET MUTATION ANALYSIS
D56V1, survival
               sevent
clus2             0   1
  RET MUTATED     4   2
  RET WILD-TYPE 374  91
  RET MUTATED RET WILD-TYPE 
            6           465 
  RET MUTATED RET WILD-TYPE 
            2            91 
$`RET MUTATED`
TCGA-DU-5852 TCGA-DU-6392 TCGA-DU-7290 TCGA-DU-A6S7 TCGA-S9-A6WL TCGA-TM-A7CA 
        6.74       211.17        10.36         7.23        31.10        34.78 

$`RET WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        6.54         8.84        90.77        30.67        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  RET MUTATED RET WILD-TYPE 
         6.74          0.03 
  RET MUTATED RET WILD-TYPE 
       211.17        182.33 
  RET MUTATED RET WILD-TYPE 
        20.73         18.61 
[1] "6.7 - 211.2 (20.7)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
               cls
clus              0   1
  RET MUTATED     4   2
  RET WILD-TYPE 203 264
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      4    2
  RET WILD-TYPE  203  264
        clus
vv       RET MUTATED RET WILD-TYPE
  FEMALE           4           203
  MALE             2           264
[1] 2 2
[1] FALSE
D56V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RET MUTATED             5                1                 0
  RET WILD-TYPE         170              118               179
D56V5, multiclass
                   clus
vv                  RET MUTATED RET WILD-TYPE
  ASTROCYTOMA                 5           170
  OLIGOASTROCYTOMA            1           118
  OLIGODENDROGLIOMA           0           179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
               cls
clus              0   1
  RET MUTATED     1   5
  RET WILD-TYPE  91 376
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      1    5
  RET WILD-TYPE   91  376
     clus
vv    RET MUTATED RET WILD-TYPE
  NO            1            91
  YES           5           376
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RET MUTATED                                  0     0
  RET WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RET MUTATED                           0     6
  RET WILD-TYPE                        15   432
D56V7, multiclass
                                  clus
vv                                 RET MUTATED RET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                      6           432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
               cls
clus              0   1
  RET MUTATED     0   6
  RET WILD-TYPE  18 414
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      0    6
  RET WILD-TYPE   18  414
                        clus
vv                       RET MUTATED RET WILD-TYPE
  HISPANIC OR LATINO               0            18
  NOT HISPANIC OR LATINO           6           414
[1] 2 2
[1] FALSE

Clustering(57) Variable = ZNF148 MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  ZNF148 MUTATED     4   0
  ZNF148 WILD-TYPE 374  93
  ZNF148 MUTATED ZNF148 WILD-TYPE 
               4              467 
  ZNF148 MUTATED ZNF148 WILD-TYPE 
               0               93 
$`ZNF148 MUTATED`
TCGA-DU-6392 TCGA-FG-7634 TCGA-HT-A619 TCGA-RY-A847 
      211.17        15.35        21.40        30.67 

$`ZNF148 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       24.99        23.97        18.44        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HT-A61B 
       16.93         1.81        16.14        16.83         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  ZNF148 MUTATED ZNF148 WILD-TYPE 
           15.35             0.03 
  ZNF148 MUTATED ZNF148 WILD-TYPE 
          211.17           182.33 
  ZNF148 MUTATED ZNF148 WILD-TYPE 
          26.035           18.610 
[1] "15.3 - 211.2 (26.0)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D57V2, continuous
D57V3, binary
                  cls
clus                 0   1
  ZNF148 MUTATED     2   2
  ZNF148 WILD-TYPE 205 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF148 MUTATED      2    2
  ZNF148 WILD-TYPE  205  264
        clus
vv       ZNF148 MUTATED ZNF148 WILD-TYPE
  FEMALE              2              205
  MALE                2              264
[1] 2 2
[1] FALSE
D57V4, continuous
[1] "Remove cluster labels:" "ZNF148 MUTATED"        
clus
  ZNF148 MUTATED ZNF148 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-HT-A61C       TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-KT-A7W1       TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-P5-A5EX       TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-P5-A5F6       TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-QH-A65V       TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-QH-A6CU       TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-QH-A6CY       TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-QH-A6X5       TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-QH-A6XC       TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-RY-A840       TCGA-RY-A845       TCGA-S9-A6TS       TCGA-S9-A6TU 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" "ZNF148 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZNF148 MUTATED             1                0                 3
  ZNF148 WILD-TYPE         174              119               176
D57V5, multiclass
                   clus
vv                  ZNF148 MUTATED ZNF148 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              3              176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                  cls
clus                 0   1
  ZNF148 MUTATED     1   3
  ZNF148 WILD-TYPE  91 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF148 MUTATED      1    3
  ZNF148 WILD-TYPE   91  378
     clus
vv    ZNF148 MUTATED ZNF148 WILD-TYPE
  NO               1               91
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF148 MUTATED                                  0     1
  ZNF148 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF148 MUTATED                           0     3
  ZNF148 WILD-TYPE                        15   435
D57V7, multiclass
                                  clus
vv                                 ZNF148 MUTATED ZNF148 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                7
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                  cls
clus                 0   1
  ZNF148 MUTATED     0   4
  ZNF148 WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF148 MUTATED      0    4
  ZNF148 WILD-TYPE   18  416
                        clus
vv                       ZNF148 MUTATED ZNF148 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(58) Variable = HDAC2 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  HDAC2 MUTATED     3   1
  HDAC2 WILD-TYPE 375  92
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              4             467 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              1              92 
$`HDAC2 MUTATED`
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-8168 TCGA-HT-7694 
      211.17        22.42        14.17         6.90 

$`HDAC2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  HDAC2 MUTATED HDAC2 WILD-TYPE 
           6.90            0.03 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
         211.17          182.33 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
         18.295          18.610 
[1] "6.9 - 211.2 (18.3)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.9"
D58V2, continuous
D58V3, binary
                 cls
clus                0   1
  HDAC2 MUTATED     2   2
  HDAC2 WILD-TYPE 205 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      2    2
  HDAC2 WILD-TYPE  205  264
        clus
vv       HDAC2 MUTATED HDAC2 WILD-TYPE
  FEMALE             2             205
  MALE               2             264
[1] 2 2
[1] FALSE
D58V4, continuous
[1] "Remove cluster labels:" "HDAC2 MUTATED"         
clus
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7854      TCGA-HT-7875      TCGA-HT-7884 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7      TCGA-HT-A5RA 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C      TCGA-HT-A74L 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1      TCGA-P5-A5EU 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" "HDAC2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HDAC2 MUTATED             1                0                 3
  HDAC2 WILD-TYPE         174              119               176
D58V5, multiclass
                   clus
vv                  HDAC2 MUTATED HDAC2 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                 cls
clus                0   1
  HDAC2 MUTATED     3   1
  HDAC2 WILD-TYPE  89 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      3    1
  HDAC2 WILD-TYPE   89  380
     clus
vv    HDAC2 MUTATED HDAC2 WILD-TYPE
  NO              3              89
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC2 MUTATED                                  0     0
  HDAC2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC2 MUTATED                           0     4
  HDAC2 WILD-TYPE                        15   434
D58V7, multiclass
                                  clus
vv                                 HDAC2 MUTATED HDAC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                 cls
clus                0   1
  HDAC2 MUTATED     0   4
  HDAC2 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      0    4
  HDAC2 WILD-TYPE   18  416
                        clus
vv                       HDAC2 MUTATED HDAC2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(59) Variable = RBBP6 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2               0   1
  RBBP6 MUTATED     5   1
  RBBP6 WILD-TYPE 373  92
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              6             465 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              1              92 
$`RBBP6 MUTATED`
TCGA-DU-6392 TCGA-DU-7010 TCGA-QH-A65Z TCGA-R8-A6MK TCGA-R8-A6MO TCGA-S9-A6WP 
      211.17        14.99        14.04        88.83        32.65        15.16 

$`RBBP6 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       11.08        12.99        94.03        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  RBBP6 MUTATED RBBP6 WILD-TYPE 
          14.04            0.03 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
         211.17          182.33 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
         23.905          18.610 
[1] "14.0 - 211.2 (23.9)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.9"
D59V2, continuous
D59V3, binary
                 cls
clus                0   1
  RBBP6 MUTATED     3   3
  RBBP6 WILD-TYPE 204 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      3    3
  RBBP6 WILD-TYPE  204  263
        clus
vv       RBBP6 MUTATED RBBP6 WILD-TYPE
  FEMALE             3             204
  MALE               3             263
[1] 2 2
[1] FALSE
D59V4, continuous
[1] "Remove cluster labels:" "RBBP6 MUTATED"         
clus
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-HT-A61C      TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-KT-A7W1      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-P5-A5F6      TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-QH-A65V      TCGA-QH-A65X      TCGA-QH-A6CS      TCGA-QH-A6CU 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" "RBBP6 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RBBP6 MUTATED             2                1                 3
  RBBP6 WILD-TYPE         173              118               176
D59V5, multiclass
                   clus
vv                  RBBP6 MUTATED RBBP6 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                 cls
clus                0   1
  RBBP6 MUTATED     1   5
  RBBP6 WILD-TYPE  91 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      1    5
  RBBP6 WILD-TYPE   91  376
     clus
vv    RBBP6 MUTATED RBBP6 WILD-TYPE
  NO              1              91
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBBP6 MUTATED                                  0     1
  RBBP6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBBP6 MUTATED                           0     5
  RBBP6 WILD-TYPE                        15   433
D59V7, multiclass
                                  clus
vv                                 RBBP6 MUTATED RBBP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               7
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                 cls
clus                0   1
  RBBP6 MUTATED     0   5
  RBBP6 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      0    5
  RBBP6 WILD-TYPE   18  415
                        clus
vv                       RBBP6 MUTATED RBBP6 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(60) Variable = MED9 MUTATION ANALYSIS
D60V1, survival
                sevent
clus2              0   1
  MED9 MUTATED     2   1
  MED9 WILD-TYPE 376  92
  MED9 MUTATED MED9 WILD-TYPE 
             3            468 
  MED9 MUTATED MED9 WILD-TYPE 
             1             92 
$`MED9 MUTATED`
TCGA-DB-A64O TCGA-DU-8163 TCGA-QH-A6CY 
       25.48        20.68         2.20 

$`MED9 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        13.61        12.23         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  MED9 MUTATED MED9 WILD-TYPE 
          2.20           0.03 
  MED9 MUTATED MED9 WILD-TYPE 
         25.48         211.17 
  MED9 MUTATED MED9 WILD-TYPE 
         20.68          18.61 
[1] "2.2 - 25.5 (20.7)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "3.4"
D60V2, continuous
D60V3, binary
                cls
clus               0   1
  MED9 MUTATED     0   3
  MED9 WILD-TYPE 207 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      0    3
  MED9 WILD-TYPE  207  263
        clus
vv       MED9 MUTATED MED9 WILD-TYPE
  FEMALE            0            207
  MALE              3            263
[1] 2 2
[1] FALSE
D60V4, continuous
[1] "Remove cluster labels:" "MED9 MUTATED"          
clus
  MED9 MUTATED MED9 WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8165     TCGA-DU-8167     TCGA-DU-8168 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS     TCGA-DU-A5TU 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6     TCGA-DU-A6S7 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6     TCGA-DU-A7T8 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC     TCGA-DU-A7TD 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311     TCGA-E1-5318 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO     TCGA-E1-A7YV 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963     TCGA-FG-5965 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690     TCGA-FG-6691 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181     TCGA-FG-8185 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3     TCGA-FG-A711 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615     TCGA-HT-A617 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CZ 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5     TCGA-QH-A6X8 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC     TCGA-QH-A86X 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840     TCGA-RY-A845 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU     TCGA-S9-A6TV 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY     TCGA-S9-A6TZ 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2     TCGA-S9-A6U5 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA     TCGA-S9-A6UB 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG     TCGA-S9-A6WH 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM     TCGA-S9-A6WN 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ     TCGA-S9-A7IQ 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MED9 MUTATED             0                3                 0
  MED9 WILD-TYPE         175              116               179
D60V5, multiclass
                   clus
vv                  MED9 MUTATED MED9 WILD-TYPE
  ASTROCYTOMA                  0            175
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                cls
clus               0   1
  MED9 MUTATED     0   3
  MED9 WILD-TYPE  92 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      0    3
  MED9 WILD-TYPE   92  378
     clus
vv    MED9 MUTATED MED9 WILD-TYPE
  NO             0             92
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED9 MUTATED                                  0     0
  MED9 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MED9 MUTATED                           0     3
  MED9 WILD-TYPE                        15   435
D60V7, multiclass
                                  clus
vv                                 MED9 MUTATED MED9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                cls
clus               0   1
  MED9 MUTATED     0   3
  MED9 WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      0    3
  MED9 WILD-TYPE   18  417
                        clus
vv                       MED9 MUTATED MED9 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(61) Variable = DDX5 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     5   0
  DDX5 WILD-TYPE 373  93
  DDX5 MUTATED DDX5 WILD-TYPE 
             5            466 
  DDX5 MUTATED DDX5 WILD-TYPE 
             0             93 
$`DDX5 MUTATED`
TCGA-CS-4943 TCGA-DU-5853 TCGA-DU-6392 TCGA-FG-8186 TCGA-HT-7687 
       18.15        13.38       211.17        16.01         0.10 

$`DDX5 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        14.24        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05        42.74        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  DDX5 MUTATED DDX5 WILD-TYPE 
          0.10           0.03 
  DDX5 MUTATED DDX5 WILD-TYPE 
        211.17         182.33 
  DDX5 MUTATED DDX5 WILD-TYPE 
         16.01          18.66 
[1] "0.1 - 211.2 (16.0)" "0.0 - 182.3 (18.7)"
[1] "hr="   "1e+07"
D61V2, continuous
D61V3, binary
                cls
clus               0   1
  DDX5 MUTATED     2   3
  DDX5 WILD-TYPE 205 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      2    3
  DDX5 WILD-TYPE  205  263
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            2            205
  MALE              3            263
[1] 2 2
[1] FALSE
D61V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DDX5 MUTATED             2                2                 1
  DDX5 WILD-TYPE         173              117               178
D61V5, multiclass
                   clus
vv                  DDX5 MUTATED DDX5 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                cls
clus               0   1
  DDX5 MUTATED     2   3
  DDX5 WILD-TYPE  90 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      2    3
  DDX5 WILD-TYPE   90  378
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             2             90
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX5 MUTATED                                  0     0
  DDX5 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDX5 MUTATED                           0     5
  DDX5 WILD-TYPE                        15   433
D61V7, multiclass
                                  clus
vv                                 DDX5 MUTATED DDX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                cls
clus               0   1
  DDX5 MUTATED     1   3
  DDX5 WILD-TYPE  17 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      1    3
  DDX5 WILD-TYPE   17  417
                        clus
vv                       DDX5 MUTATED DDX5 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(62) Variable = ZC3H11A MUTATION ANALYSIS
D62V1, survival
                   sevent
clus2                 0   1
  ZC3H11A MUTATED     1   4
  ZC3H11A WILD-TYPE 377  89
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               466 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                4                89 
$`ZC3H11A MUTATED`
TCGA-DU-6392 TCGA-DU-A7TD TCGA-FG-A4MW TCGA-QH-A6CX TCGA-TM-A84B 
      211.17         7.50        18.38        12.23        24.92 

$`ZC3H11A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       17.98       124.50        77.88        42.31        23.51        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        13.61         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       49.45        48.33        49.32        34.78        48.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
             7.50              0.03 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
           211.17            182.33 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            18.38             18.61 
[1] "7.5 - 211.2 (18.4)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.2"
D62V2, continuous
D62V3, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     1   4
  ZC3H11A WILD-TYPE 206 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      1    4
  ZC3H11A WILD-TYPE  206  262
        clus
vv       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  FEMALE               1               206
  MALE                 4               262
[1] 2 2
[1] FALSE
D62V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZC3H11A MUTATED             3                2                 0
  ZC3H11A WILD-TYPE         172              117               179
D62V5, multiclass
                   clus
vv                  ZC3H11A MUTATED ZC3H11A WILD-TYPE
  ASTROCYTOMA                     3               172
  OLIGOASTROCYTOMA                2               117
  OLIGODENDROGLIOMA               0               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     1   4
  ZC3H11A WILD-TYPE  91 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      1    4
  ZC3H11A WILD-TYPE   91  377
     clus
vv    ZC3H11A MUTATED ZC3H11A WILD-TYPE
  NO                1                91
  YES               4               377
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H11A MUTATED                                  0     0
  ZC3H11A WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZC3H11A MUTATED                           0     5
  ZC3H11A WILD-TYPE                        15   433
D62V7, multiclass
                                  clus
vv                                 ZC3H11A MUTATED ZC3H11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          5               433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     0   5
  ZC3H11A WILD-TYPE  18 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      0    5
  ZC3H11A WILD-TYPE   18  415
                        clus
vv                       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               5               415
[1] 2 2
[1] FALSE

Clustering(63) Variable = SLC6A3 MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2                0   1
  SLC6A3 MUTATED     7   2
  SLC6A3 WILD-TYPE 371  91
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               9              462 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               2               91 
$`SLC6A3 MUTATED`
TCGA-DB-A4XD TCGA-DU-6392 TCGA-DU-6400 TCGA-HT-7471 TCGA-HT-7855 TCGA-HT-7882 
       39.78       211.17         1.22         0.13        19.23         3.72 
TCGA-HT-8105 TCGA-HW-A5KL TCGA-WY-A85E 
        6.25        20.81        20.81 

$`SLC6A3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        46.72        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       11.54        40.11         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        37.87        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       20.35        12.76        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
            0.13             0.03 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
          211.17           182.33 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
           19.23            18.61 
[1] "0.1 - 211.2 (19.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D63V2, continuous
D63V3, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     5   4
  SLC6A3 WILD-TYPE 202 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      5    4
  SLC6A3 WILD-TYPE  202  262
        clus
vv       SLC6A3 MUTATED SLC6A3 WILD-TYPE
  FEMALE              5              202
  MALE                4              262
[1] 2 2
[1] FALSE
D63V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SLC6A3 MUTATED             4                1                 4
  SLC6A3 WILD-TYPE         171              118               175
D63V5, multiclass
                   clus
vv                  SLC6A3 MUTATED SLC6A3 WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              4              175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     2   7
  SLC6A3 WILD-TYPE  90 374
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      2    7
  SLC6A3 WILD-TYPE   90  374
     clus
vv    SLC6A3 MUTATED SLC6A3 WILD-TYPE
  NO               2               90
  YES              7              374
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A3 MUTATED                                  0     0
  SLC6A3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC6A3 MUTATED                           0     9
  SLC6A3 WILD-TYPE                        15   429
D63V7, multiclass
                                  clus
vv                                 SLC6A3 MUTATED SLC6A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         9              429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     1   6
  SLC6A3 WILD-TYPE  17 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      1    6
  SLC6A3 WILD-TYPE   17  414
                        clus
vv                       SLC6A3 MUTATED SLC6A3 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              6              414
[1] 2 2
[1] FALSE

Clustering(64) Variable = TPTE2 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED     5   0
  TPTE2 WILD-TYPE 373  93
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              5             466 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              0              93 
$`TPTE2 MUTATED`
TCGA-DU-5871 TCGA-HW-A5KM TCGA-QH-A65S TCGA-TM-A7CA TCGA-TM-A84H 
       18.94        20.71         2.53        34.78        30.44 

$`TPTE2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       20.35        12.76        20.81        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        48.33        49.32        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           2.53            0.03 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          34.78          211.17 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          20.71           18.56 
[1] "2.5 - 34.8 (20.7)"  "0.0 - 211.2 (18.6)"
[1] "hr="     "3300000"
D64V2, continuous
D64V3, binary
                 cls
clus                0   1
  TPTE2 MUTATED     3   2
  TPTE2 WILD-TYPE 204 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      3    2
  TPTE2 WILD-TYPE  204  264
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             3             204
  MALE               2             264
[1] 2 2
[1] FALSE
D64V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TPTE2 MUTATED             2                3                 0
  TPTE2 WILD-TYPE         173              116               179
D64V5, multiclass
                   clus
vv                  TPTE2 MUTATED TPTE2 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0   5
  TPTE2 WILD-TYPE  92 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0    5
  TPTE2 WILD-TYPE   92  376
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO              0              92
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPTE2 MUTATED                                  0     0
  TPTE2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED                           0     5
  TPTE2 WILD-TYPE                        15   433
D64V7, multiclass
                                  clus
vv                                 TPTE2 MUTATED TPTE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0   4
  TPTE2 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0    4
  TPTE2 WILD-TYPE   18  416
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(65) Variable = C4BPA MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  C4BPA MUTATED     3   1
  C4BPA WILD-TYPE 375  92
  C4BPA MUTATED C4BPA WILD-TYPE 
              4             467 
  C4BPA MUTATED C4BPA WILD-TYPE 
              1              92 
$`C4BPA MUTATED`
TCGA-DU-6392 TCGA-DU-8162 TCGA-S9-A7QX TCGA-TM-A84Q 
      211.17        14.60        13.12        25.38 

$`C4BPA WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        17.03        15.06        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  C4BPA MUTATED C4BPA WILD-TYPE 
          13.12            0.03 
  C4BPA MUTATED C4BPA WILD-TYPE 
         211.17          182.33 
  C4BPA MUTATED C4BPA WILD-TYPE 
          19.99           18.61 
[1] "13.1 - 211.2 (20.0)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2"  
D65V2, continuous
D65V3, binary
                 cls
clus                0   1
  C4BPA MUTATED     3   1
  C4BPA WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C4BPA MUTATED      3    1
  C4BPA WILD-TYPE  204  265
        clus
vv       C4BPA MUTATED C4BPA WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D65V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  C4BPA MUTATED             3                1                 0
  C4BPA WILD-TYPE         172              118               179
D65V5, multiclass
                   clus
vv                  C4BPA MUTATED C4BPA WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                 cls
clus                0   1
  C4BPA MUTATED     1   3
  C4BPA WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C4BPA MUTATED      1    3
  C4BPA WILD-TYPE   91  378
     clus
vv    C4BPA MUTATED C4BPA WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C4BPA MUTATED                                  0     0
  C4BPA WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C4BPA MUTATED                           0     4
  C4BPA WILD-TYPE                        15   434
D65V7, multiclass
                                  clus
vv                                 C4BPA MUTATED C4BPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                 cls
clus                0   1
  C4BPA MUTATED     0   4
  C4BPA WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C4BPA MUTATED      0    4
  C4BPA WILD-TYPE   18  416
                        clus
vv                       C4BPA MUTATED C4BPA WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(66) Variable = MATK MUTATION ANALYSIS
D66V1, survival
                sevent
clus2              0   1
  MATK MUTATED     4   1
  MATK WILD-TYPE 374  92
  MATK MUTATED MATK WILD-TYPE 
             5            466 
  MATK MUTATED MATK WILD-TYPE 
             1             92 
$`MATK MUTATED`
TCGA-CS-6670 TCGA-DB-5277 TCGA-DH-A7US TCGA-DU-6392 TCGA-HT-7690 
        6.61        50.86        13.12       211.17         0.10 

$`MATK WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  MATK MUTATED MATK WILD-TYPE 
          0.10           0.03 
  MATK MUTATED MATK WILD-TYPE 
        211.17         182.33 
  MATK MUTATED MATK WILD-TYPE 
         13.12          18.61 
[1] "0.1 - 211.2 (13.1)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.2"
D66V2, continuous
D66V3, binary
                cls
clus               0   1
  MATK MUTATED     1   4
  MATK WILD-TYPE 206 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  MATK MUTATED      1    4
  MATK WILD-TYPE  206  262
        clus
vv       MATK MUTATED MATK WILD-TYPE
  FEMALE            1            206
  MALE              4            262
[1] 2 2
[1] FALSE
D66V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MATK MUTATED             2                1                 2
  MATK WILD-TYPE         173              118               177
D66V5, multiclass
                   clus
vv                  MATK MUTATED MATK WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             1            118
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                cls
clus               0   1
  MATK MUTATED     3   2
  MATK WILD-TYPE  89 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  MATK MUTATED      3    2
  MATK WILD-TYPE   89  379
     clus
vv    MATK MUTATED MATK WILD-TYPE
  NO             3             89
  YES            2            379
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MATK MUTATED                                  0     0
  MATK WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MATK MUTATED                           0     5
  MATK WILD-TYPE                        15   433
D66V7, multiclass
                                  clus
vv                                 MATK MUTATED MATK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                cls
clus               0   1
  MATK MUTATED     0   5
  MATK WILD-TYPE  18 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  MATK MUTATED      0    5
  MATK WILD-TYPE   18  415
                        clus
vv                       MATK MUTATED MATK WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            415
[1] 2 2
[1] FALSE

Clustering(67) Variable = SMOC1 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  SMOC1 MUTATED     3   0
  SMOC1 WILD-TYPE 375  93
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              3             468 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              0              93 
$`SMOC1 MUTATED`
TCGA-CS-4944 TCGA-HT-7475 TCGA-WY-A858 
       10.62        17.42        43.96 

$`SMOC1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  SMOC1 MUTATED SMOC1 WILD-TYPE 
          10.62            0.03 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
          43.96          211.17 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
          17.42           18.61 
[1] "10.6 - 44.0 (17.4)" "0.0 - 211.2 (18.6)"
[1] "hr="     "3300000"
D67V2, continuous
D67V3, binary
                 cls
clus                0   1
  SMOC1 MUTATED     1   2
  SMOC1 WILD-TYPE 206 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      1    2
  SMOC1 WILD-TYPE  206  264
        clus
vv       SMOC1 MUTATED SMOC1 WILD-TYPE
  FEMALE             1             206
  MALE               2             264
[1] 2 2
[1] FALSE
D67V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SMOC1 MUTATED             2                1                 0
  SMOC1 WILD-TYPE         173              118               179
D67V5, multiclass
                   clus
vv                  SMOC1 MUTATED SMOC1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                 cls
clus                0   1
  SMOC1 MUTATED     2   1
  SMOC1 WILD-TYPE  90 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      2    1
  SMOC1 WILD-TYPE   90  380
     clus
vv    SMOC1 MUTATED SMOC1 WILD-TYPE
  NO              2              90
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMOC1 MUTATED                                  0     0
  SMOC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMOC1 MUTATED                           0     3
  SMOC1 WILD-TYPE                        15   435
D67V7, multiclass
                                  clus
vv                                 SMOC1 MUTATED SMOC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                 cls
clus                0   1
  SMOC1 MUTATED     0   1
  SMOC1 WILD-TYPE  18 419
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      0    1
  SMOC1 WILD-TYPE   18  419
                        clus
vv                       SMOC1 MUTATED SMOC1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             1             419
[1] 2 2
[1] FALSE

Clustering(68) Variable = NAP1L2 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  NAP1L2 MUTATED     4   0
  NAP1L2 WILD-TYPE 374  93
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               4              467 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               0               93 
$`NAP1L2 MUTATED`
TCGA-DH-A7UR TCGA-FG-A710 TCGA-HT-8114 TCGA-WY-A85D 
       54.25        36.66        34.19        37.71 

$`NAP1L2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        27.81        17.19        17.19        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8558 
        2.50         5.56        13.78         0.23        29.59        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        20.81 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           34.19             0.03 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           54.25           211.17 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
          37.185           18.510 
[1] "34.2 - 54.2 (37.2)" "0.0 - 211.2 (18.5)"
[1] "hr="     "9100000"
D68V2, continuous
D68V3, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     2   2
  NAP1L2 WILD-TYPE 205 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      2    2
  NAP1L2 WILD-TYPE  205  264
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              2              205
  MALE                2              264
[1] 2 2
[1] FALSE
D68V4, continuous
[1] "Remove cluster labels:" "NAP1L2 MUTATED"        
clus
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UU       TCGA-DH-A7UV 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853       TCGA-DU-5854 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871       TCGA-DU-5874 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404       TCGA-DU-6405 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410       TCGA-DU-7011 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299       TCGA-DU-7300 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304       TCGA-DU-7306 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161       TCGA-DU-8162 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167       TCGA-DU-8168 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TU 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6       TCGA-DU-A6S7 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6       TCGA-DU-A7T8 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC       TCGA-DU-A7TD 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO       TCGA-E1-A7YV 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963       TCGA-FG-5965 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NAP1L2 MUTATED             0                2                 2
  NAP1L2 WILD-TYPE         175              117               177
D68V5, multiclass
                   clus
vv                  NAP1L2 MUTATED NAP1L2 WILD-TYPE
  ASTROCYTOMA                    0              175
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              2              177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     1   3
  NAP1L2 WILD-TYPE  91 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      1    3
  NAP1L2 WILD-TYPE   91  378
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               1               91
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L2 MUTATED                                  0     0
  NAP1L2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L2 MUTATED                           0     4
  NAP1L2 WILD-TYPE                        15   434
D68V7, multiclass
                                  clus
vv                                 NAP1L2 MUTATED NAP1L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     0   3
  NAP1L2 WILD-TYPE  18 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      0    3
  NAP1L2 WILD-TYPE   18  417
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              3              417
[1] 2 2
[1] FALSE

Clustering(69) Variable = CD99L2 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  CD99L2 MUTATED     3   0
  CD99L2 WILD-TYPE 375  93
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               3              468 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               0               93 
$`CD99L2 MUTATED`
TCGA-DU-6392 TCGA-FG-8189 TCGA-HT-7471 
      211.17        22.52         0.13 

$`CD99L2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        14.96        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54        40.11         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  CD99L2 MUTATED CD99L2 WILD-TYPE 
            0.13             0.03 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
          211.17           182.33 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
           22.52            18.61 
[1] "0.1 - 211.2 (22.5)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D69V2, continuous
D69V3, binary
                  cls
clus                 0   1
  CD99L2 MUTATED     3   0
  CD99L2 WILD-TYPE 204 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      3    0
  CD99L2 WILD-TYPE  204  266
        clus
vv       CD99L2 MUTATED CD99L2 WILD-TYPE
  FEMALE              3              204
  MALE                0              266
[1] 2 2
[1] FALSE
D69V4, continuous
[1] "Remove cluster labels:" "CD99L2 MUTATED"        
clus
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" "CD99L2 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CD99L2 MUTATED             1                0                 2
  CD99L2 WILD-TYPE         174              119               177
D69V5, multiclass
                   clus
vv                  CD99L2 MUTATED CD99L2 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              2              177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                  cls
clus                 0   1
  CD99L2 MUTATED     1   2
  CD99L2 WILD-TYPE  91 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      1    2
  CD99L2 WILD-TYPE   91  379
     clus
vv    CD99L2 MUTATED CD99L2 WILD-TYPE
  NO               1               91
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD99L2 MUTATED                                  0     0
  CD99L2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CD99L2 MUTATED                           0     3
  CD99L2 WILD-TYPE                        15   435
D69V7, multiclass
                                  clus
vv                                 CD99L2 MUTATED CD99L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                  cls
clus                 0   1
  CD99L2 MUTATED     0   3
  CD99L2 WILD-TYPE  18 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      0    3
  CD99L2 WILD-TYPE   18  417
                        clus
vv                       CD99L2 MUTATED CD99L2 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              3              417
[1] 2 2
[1] FALSE

Clustering(70) Variable = SELE MUTATION ANALYSIS
D70V1, survival
                sevent
clus2              0   1
  SELE MUTATED     3   3
  SELE WILD-TYPE 375  90
  SELE MUTATED SELE WILD-TYPE 
             6            465 
  SELE MUTATED SELE WILD-TYPE 
             3             90 
$`SELE MUTATED`
TCGA-CS-6186 TCGA-CS-6665 TCGA-DU-6392 TCGA-DU-A76K TCGA-E1-5318 TCGA-TM-A84H 
       17.69        12.43       211.17        11.41        78.21        30.44 

$`SELE WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
       40.18         0.10        21.01         9.96         6.38        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 
       67.46        41.13        79.99        57.93       134.27        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  SELE MUTATED SELE WILD-TYPE 
         11.41           0.03 
  SELE MUTATED SELE WILD-TYPE 
        211.17         182.33 
  SELE MUTATED SELE WILD-TYPE 
        24.065         18.610 
[1] "11.4 - 211.2 (24.1)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                cls
clus               0   1
  SELE MUTATED     4   2
  SELE WILD-TYPE 203 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      4    2
  SELE WILD-TYPE  203  264
        clus
vv       SELE MUTATED SELE WILD-TYPE
  FEMALE            4            203
  MALE              2            264
[1] 2 2
[1] FALSE
D70V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SELE MUTATED             2                2                 2
  SELE WILD-TYPE         173              117               177
D70V5, multiclass
                   clus
vv                  SELE MUTATED SELE WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                cls
clus               0   1
  SELE MUTATED     2   4
  SELE WILD-TYPE  90 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      2    4
  SELE WILD-TYPE   90  377
     clus
vv    SELE MUTATED SELE WILD-TYPE
  NO             2             90
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SELE MUTATED                                  0     0
  SELE WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SELE MUTATED                           0     6
  SELE WILD-TYPE                        15   432
D70V7, multiclass
                                  clus
vv                                 SELE MUTATED SELE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       6            432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                cls
clus               0   1
  SELE MUTATED     0   6
  SELE WILD-TYPE  18 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      0    6
  SELE WILD-TYPE   18  414
                        clus
vv                       SELE MUTATED SELE WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            6            414
[1] 2 2
[1] FALSE

Clustering(71) Variable = TMEM184A MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  TMEM184A MUTATED     2   1
  TMEM184A WILD-TYPE 376  92
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 3                468 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 1                 92 
$`TMEM184A MUTATED`
TCGA-DU-7012 TCGA-HT-7875 TCGA-QH-A6CZ 
        6.54         0.33         9.17 

$`TMEM184A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99       105.21         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
       14.83        14.53        13.61        12.23         2.20        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  TMEM184A MUTATED TMEM184A WILD-TYPE 
              0.33               0.03 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
              9.17             211.17 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
              6.54              18.66 
[1] "0.3 - 9.2 (6.5)"    "0.0 - 211.2 (18.7)"
[1] "hr=" "15" 
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  TMEM184A MUTATED     1   2
  TMEM184A WILD-TYPE 206 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      1    2
  TMEM184A WILD-TYPE  206  264
        clus
vv       TMEM184A MUTATED TMEM184A WILD-TYPE
  FEMALE                1                206
  MALE                  2                264
[1] 2 2
[1] FALSE
D71V4, continuous
[1] "Remove cluster labels:" "TMEM184A MUTATED"      
clus
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 2                267 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6188 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-CS-6290         TCGA-CS-6665         TCGA-CS-6666 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-CS-6667         TCGA-CS-6668         TCGA-CS-6669 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-A4XE         TCGA-DB-A64L 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DB-A64Q         TCGA-DB-A64R         TCGA-DB-A64S 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DB-A64U         TCGA-DB-A64V         TCGA-DB-A64W 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DB-A64X         TCGA-DB-A75L         TCGA-DB-A75O 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5142         TCGA-DH-5143 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DH-A7UR 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DH-A7UU         TCGA-DH-A7UV         TCGA-DU-5851 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-5874         TCGA-DU-6396         TCGA-DU-6403 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-6404         TCGA-DU-6405         TCGA-DU-6407 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-6408         TCGA-DU-6410         TCGA-DU-7011 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7015         TCGA-DU-7018 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-7019         TCGA-DU-7294         TCGA-DU-7298 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-7299         TCGA-DU-7300         TCGA-DU-7301 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-7302         TCGA-DU-7304         TCGA-DU-7306 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-7309         TCGA-DU-8158         TCGA-DU-8161 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-8162         TCGA-DU-8163         TCGA-DU-8165 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-8167         TCGA-DU-8168         TCGA-DU-A5TP 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A5TR         TCGA-DU-A5TS         TCGA-DU-A5TU 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A5TW         TCGA-DU-A6S2         TCGA-DU-A6S6 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A6S7         TCGA-DU-A6S8         TCGA-DU-A76R 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A7T6         TCGA-DU-A7T8         TCGA-DU-A7TA 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A7TB         TCGA-DU-A7TC         TCGA-DU-A7TD 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-DU-A7TG         TCGA-E1-5302         TCGA-E1-5303 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5305         TCGA-E1-5307 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-E1-5311         TCGA-E1-5318         TCGA-E1-5319 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-E1-5322         TCGA-E1-A7YO         TCGA-E1-A7YV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-E1-A7YW         TCGA-E1-A7Z6         TCGA-FG-5963 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-5965         TCGA-FG-6688         TCGA-FG-6689 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-6690         TCGA-FG-6691         TCGA-FG-7636 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-7638         TCGA-FG-8181         TCGA-FG-8185 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-8186         TCGA-FG-8187         TCGA-FG-8188 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-8189         TCGA-FG-A4MT         TCGA-FG-A4MW 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-A4MX         TCGA-FG-A60J         TCGA-FG-A60L 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-A6J1         TCGA-FG-A6J3         TCGA-FG-A711 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FG-A713         TCGA-FG-A87Q         TCGA-HT-7468 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-7470         TCGA-HT-7475         TCGA-HT-7477 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7607         TCGA-HT-7609 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-7611         TCGA-HT-7689         TCGA-HT-7692 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-7693         TCGA-HT-7694         TCGA-HT-7854 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-7884         TCGA-HT-8564         TCGA-HT-A4DV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-A5R7         TCGA-HT-A5RA         TCGA-HT-A5RC 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-A615         TCGA-HT-A617         TCGA-HT-A618 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-A61A         TCGA-HT-A61B         TCGA-HT-A61C 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HT-A74L         TCGA-IK-7675         TCGA-KT-A74X 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-KT-A7W1         TCGA-P5-A5EU         TCGA-P5-A5EV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-P5-A5EW         TCGA-P5-A5EX         TCGA-P5-A5F0 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-P5-A5F2         TCGA-P5-A5F4         TCGA-P5-A5F6 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-P5-A731         TCGA-QH-A65R         TCGA-QH-A65S 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A65V         TCGA-QH-A65X         TCGA-QH-A65Z 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A6CS         TCGA-QH-A6CU         TCGA-QH-A6CV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A6CW         TCGA-QH-A6CX         TCGA-QH-A6CY 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A6X3         TCGA-QH-A6X4         TCGA-QH-A6X5 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A6X8         TCGA-QH-A6X9         TCGA-QH-A6XA 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-QH-A6XC         TCGA-QH-A86X         TCGA-QH-A870 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-RY-A83Y         TCGA-RY-A840         TCGA-RY-A845 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-RY-A847         TCGA-S9-A6TS         TCGA-S9-A6TU 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6TV         TCGA-S9-A6TW         TCGA-S9-A6TX 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6TY         TCGA-S9-A6TZ         TCGA-S9-A6U0 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6U1         TCGA-S9-A6U2         TCGA-S9-A6U5 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6U6         TCGA-S9-A6U8         TCGA-S9-A6UA 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6UB         TCGA-S9-A6WD         TCGA-S9-A6WE 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6WG         TCGA-S9-A6WH         TCGA-S9-A6WI 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6WL         TCGA-S9-A6WM         TCGA-S9-A6WN 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A6WO         TCGA-S9-A6WP         TCGA-S9-A6WQ 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7IQ         TCGA-S9-A7IS         TCGA-S9-A7IX 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7IY         TCGA-S9-A7IZ         TCGA-S9-A7J0 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7J1         TCGA-S9-A7J2         TCGA-S9-A7J3 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7QW         TCGA-S9-A7QX         TCGA-S9-A7QY 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7QZ         TCGA-S9-A7R1         TCGA-S9-A7R2 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7R3         TCGA-S9-A7R4         TCGA-S9-A7R7 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-S9-A7R8         TCGA-S9-A89V         TCGA-S9-A89Z 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A7C3         TCGA-TM-A7C4         TCGA-TM-A7C5 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A7CA         TCGA-TM-A7CF         TCGA-TM-A84B 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A84C         TCGA-TM-A84F         TCGA-TM-A84G 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A84H         TCGA-TM-A84I         TCGA-TM-A84J 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A84L         TCGA-TM-A84M         TCGA-TM-A84O 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A84Q         TCGA-TM-A84R         TCGA-TM-A84S 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-TM-A84T         TCGA-TQ-A7RW         TCGA-VM-A8C8 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-VM-A8CA         TCGA-VM-A8CD         TCGA-VM-A8CE 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-VM-A8CH         TCGA-WY-A858         TCGA-WY-A859 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TMEM184A MUTATED             1                1                 1
  TMEM184A WILD-TYPE         174              118               178
D71V5, multiclass
                   clus
vv                  TMEM184A MUTATED TMEM184A WILD-TYPE
  ASTROCYTOMA                      1                174
  OLIGOASTROCYTOMA                 1                118
  OLIGODENDROGLIOMA                1                178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  TMEM184A MUTATED     1   2
  TMEM184A WILD-TYPE  91 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      1    2
  TMEM184A WILD-TYPE   91  379
     clus
vv    TMEM184A MUTATED TMEM184A WILD-TYPE
  NO                 1                 91
  YES                2                379
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM184A MUTATED                                  0     0
  TMEM184A WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM184A MUTATED                           1     2
  TMEM184A WILD-TYPE                        14   436
D71V7, multiclass
                                  clus
vv                                 TMEM184A MUTATED TMEM184A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  8
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           2                436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                   0   1
  TMEM184A MUTATED     0   3
  TMEM184A WILD-TYPE  18 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      0    3
  TMEM184A WILD-TYPE   18  417
                        clus
vv                       TMEM184A MUTATED TMEM184A WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                3                417
[1] 2 2
[1] FALSE

Clustering(72) Variable = FHOD1 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  FHOD1 MUTATED     5   1
  FHOD1 WILD-TYPE 373  92
  FHOD1 MUTATED FHOD1 WILD-TYPE 
              6             465 
  FHOD1 MUTATED FHOD1 WILD-TYPE 
              1              92 
$`FHOD1 MUTATED`
TCGA-DB-A75K TCGA-DU-6392 TCGA-DU-A6S3 TCGA-DU-A7T8 TCGA-HT-A4DV TCGA-HW-A5KK 
       12.10       211.17         2.70       124.50        26.04        12.76 

$`FHOD1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65        12.20         8.65        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30        17.98        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        20.35        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  FHOD1 MUTATED FHOD1 WILD-TYPE 
           2.70            0.03 
  FHOD1 MUTATED FHOD1 WILD-TYPE 
         211.17          182.33 
  FHOD1 MUTATED FHOD1 WILD-TYPE 
          19.40           18.61 
[1] "2.7 - 211.2 (19.4)" "0.0 - 182.3 (18.6)"
[1] "hr=" "3.1"
D72V2, continuous
D72V3, binary
                 cls
clus                0   1
  FHOD1 MUTATED     3   3
  FHOD1 WILD-TYPE 204 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD1 MUTATED      3    3
  FHOD1 WILD-TYPE  204  263
        clus
vv       FHOD1 MUTATED FHOD1 WILD-TYPE
  FEMALE             3             204
  MALE               3             263
[1] 2 2
[1] FALSE
D72V4, continuous
[1] "Remove cluster labels:" "FHOD1 MUTATED"         
clus
  FHOD1 MUTATED FHOD1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A5R7      TCGA-HT-A5RA 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C      TCGA-HT-A74L 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1      TCGA-P5-A5EU 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" "FHOD1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FHOD1 MUTATED             2                2                 2
  FHOD1 WILD-TYPE         173              117               177
D72V5, multiclass
                   clus
vv                  FHOD1 MUTATED FHOD1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                 cls
clus                0   1
  FHOD1 MUTATED     1   5
  FHOD1 WILD-TYPE  91 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD1 MUTATED      1    5
  FHOD1 WILD-TYPE   91  376
     clus
vv    FHOD1 MUTATED FHOD1 WILD-TYPE
  NO              1              91
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FHOD1 MUTATED                                  0     0
  FHOD1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FHOD1 MUTATED                           0     6
  FHOD1 WILD-TYPE                        15   432
D72V7, multiclass
                                  clus
vv                                 FHOD1 MUTATED FHOD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                 cls
clus                0   1
  FHOD1 MUTATED     0   5
  FHOD1 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD1 MUTATED      0    5
  FHOD1 WILD-TYPE   18  415
                        clus
vv                       FHOD1 MUTATED FHOD1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(73) Variable = HTR3A MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2               0   1
  HTR3A MUTATED     5   2
  HTR3A WILD-TYPE 373  91
  HTR3A MUTATED HTR3A WILD-TYPE 
              7             464 
  HTR3A MUTATED HTR3A WILD-TYPE 
              2              91 
$`HTR3A MUTATED`
TCGA-DB-5279 TCGA-DU-5852 TCGA-DU-6392 TCGA-HT-8013 TCGA-R8-A6MO TCGA-S9-A6WN 
       44.52         6.74       211.17        63.55        32.65        15.91 
TCGA-VW-A7QS 
       23.21 

$`HTR3A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        50.17        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       12.99        88.83        94.03        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        19.86        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A8FI TCGA-W9-A837 
       35.93        23.47        37.05        16.01         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  HTR3A MUTATED HTR3A WILD-TYPE 
           6.74            0.03 
  HTR3A MUTATED HTR3A WILD-TYPE 
         211.17          182.33 
  HTR3A MUTATED HTR3A WILD-TYPE 
          32.65           18.56 
[1] "6.7 - 211.2 (32.6)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
                 cls
clus                0   1
  HTR3A MUTATED     6   1
  HTR3A WILD-TYPE 201 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3A MUTATED      6    1
  HTR3A WILD-TYPE  201  265
        clus
vv       HTR3A MUTATED HTR3A WILD-TYPE
  FEMALE             6             201
  MALE               1             265
[1] 2 2
[1] FALSE
D73V4, continuous
[1] "Remove cluster labels:" "HTR3A MUTATED"         
clus
  HTR3A MUTATED HTR3A WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5853      TCGA-DU-5854 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5874 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"HTR3A WILD-TYPE" "HTR3A WILD-TYPE" "HTR3A WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HTR3A MUTATED             2                2                 3
  HTR3A WILD-TYPE         173              117               176
D73V5, multiclass
                   clus
vv                  HTR3A MUTATED HTR3A WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                 cls
clus                0   1
  HTR3A MUTATED     1   6
  HTR3A WILD-TYPE  91 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3A MUTATED      1    6
  HTR3A WILD-TYPE   91  375
     clus
vv    HTR3A MUTATED HTR3A WILD-TYPE
  NO              1              91
  YES             6             375
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTR3A MUTATED                                  0     2
  HTR3A WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTR3A MUTATED                           0     4
  HTR3A WILD-TYPE                        15   434
D73V7, multiclass
                                  clus
vv                                 HTR3A MUTATED HTR3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               6
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                 cls
clus                0   1
  HTR3A MUTATED     0   5
  HTR3A WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3A MUTATED      0    5
  HTR3A WILD-TYPE   18  415
                        clus
vv                       HTR3A MUTATED HTR3A WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(74) Variable = RB1 MUTATION ANALYSIS
D74V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     3   2
  RB1 WILD-TYPE 375  91
  RB1 MUTATED RB1 WILD-TYPE 
            5           466 
  RB1 MUTATED RB1 WILD-TYPE 
            2            91 
$`RB1 MUTATED`
TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-6392 TCGA-DU-7290 TCGA-FG-6688 
       30.21        18.02       211.17        10.36        18.77 

$`RB1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.45        18.61        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        30.67        26.30         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       36.82        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  RB1 MUTATED RB1 WILD-TYPE 
        10.36          0.03 
  RB1 MUTATED RB1 WILD-TYPE 
       211.17        182.33 
  RB1 MUTATED RB1 WILD-TYPE 
        18.77         18.61 
[1] "10.4 - 211.2 (18.8)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "1"  
D74V2, continuous
D74V3, binary
               cls
clus              0   1
  RB1 MUTATED     4   1
  RB1 WILD-TYPE 203 265
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      4    1
  RB1 WILD-TYPE  203  265
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           4           203
  MALE             1           265
[1] 2 2
[1] FALSE
D74V4, continuous
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1           268 
   TCGA-CS-4938    TCGA-CS-4941    TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-CS-5390    TCGA-CS-5393    TCGA-CS-5395    TCGA-CS-5396    TCGA-CS-5397 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-CS-6186    TCGA-CS-6188    TCGA-CS-6290    TCGA-CS-6665    TCGA-CS-6666 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-CS-6667    TCGA-CS-6668    TCGA-CS-6669    TCGA-DB-5274    TCGA-DB-A4XE 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DB-A64L    TCGA-DB-A64Q    TCGA-DB-A64R    TCGA-DB-A64S    TCGA-DB-A64U 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DB-A64V    TCGA-DB-A64W    TCGA-DB-A64X    TCGA-DB-A75L    TCGA-DB-A75O 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DH-5140    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-DH-A66B 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DH-A66D    TCGA-DH-A66F    TCGA-DH-A66G    TCGA-DH-A7UR    TCGA-DH-A7UU 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DH-A7UV    TCGA-DU-5851    TCGA-DU-5852    TCGA-DU-5853    TCGA-DU-5854 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-5855    TCGA-DU-5870    TCGA-DU-5871    TCGA-DU-5874    TCGA-DU-6396 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-6403    TCGA-DU-6404    TCGA-DU-6405    TCGA-DU-6407    TCGA-DU-6408 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-6410    TCGA-DU-7011    TCGA-DU-7013    TCGA-DU-7015    TCGA-DU-7018 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-7019    TCGA-DU-7294    TCGA-DU-7298    TCGA-DU-7299    TCGA-DU-7300 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-7301    TCGA-DU-7302    TCGA-DU-7304    TCGA-DU-7306    TCGA-DU-7309 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-8158    TCGA-DU-8161    TCGA-DU-8162    TCGA-DU-8163    TCGA-DU-8165 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-8167    TCGA-DU-8168    TCGA-DU-A5TP    TCGA-DU-A5TR    TCGA-DU-A5TS 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-A5TU    TCGA-DU-A5TW    TCGA-DU-A6S2    TCGA-DU-A6S6    TCGA-DU-A6S7 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-A6S8    TCGA-DU-A76R    TCGA-DU-A7T6    TCGA-DU-A7T8    TCGA-DU-A7TA 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-DU-A7TB    TCGA-DU-A7TC    TCGA-DU-A7TD    TCGA-DU-A7TG    TCGA-E1-5302 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5305    TCGA-E1-5307    TCGA-E1-5311 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-E1-5318    TCGA-E1-5319    TCGA-E1-5322    TCGA-E1-A7YO    TCGA-E1-A7YV 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-E1-A7YW    TCGA-E1-A7Z6    TCGA-FG-5963    TCGA-FG-5965    TCGA-FG-6689 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-FG-6690    TCGA-FG-6691    TCGA-FG-7636    TCGA-FG-7638    TCGA-FG-8181 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-FG-8185    TCGA-FG-8186    TCGA-FG-8187    TCGA-FG-8188    TCGA-FG-8189 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-FG-A4MT    TCGA-FG-A4MW    TCGA-FG-A4MX    TCGA-FG-A60J    TCGA-FG-A60L 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-FG-A6J1    TCGA-FG-A6J3    TCGA-FG-A711    TCGA-FG-A713    TCGA-FG-A87Q 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-7468    TCGA-HT-7470    TCGA-HT-7475    TCGA-HT-7477    TCGA-HT-7485 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-7607    TCGA-HT-7609    TCGA-HT-7611    TCGA-HT-7689    TCGA-HT-7692 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-7693    TCGA-HT-7694    TCGA-HT-7854    TCGA-HT-7875    TCGA-HT-7884 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-8564    TCGA-HT-A4DV    TCGA-HT-A5R7    TCGA-HT-A5RA    TCGA-HT-A5RC 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-A615    TCGA-HT-A617    TCGA-HT-A618    TCGA-HT-A61A    TCGA-HT-A61B 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-HT-A61C    TCGA-HT-A74L    TCGA-IK-7675    TCGA-KT-A74X    TCGA-KT-A7W1 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-P5-A5EU    TCGA-P5-A5EV    TCGA-P5-A5EW    TCGA-P5-A5EX    TCGA-P5-A5F0 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-P5-A5F2    TCGA-P5-A5F4    TCGA-P5-A5F6    TCGA-P5-A731    TCGA-QH-A65R 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-QH-A65S    TCGA-QH-A65V    TCGA-QH-A65X    TCGA-QH-A65Z    TCGA-QH-A6CS 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-QH-A6CU    TCGA-QH-A6CV    TCGA-QH-A6CW    TCGA-QH-A6CX    TCGA-QH-A6CY 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-QH-A6CZ    TCGA-QH-A6X3    TCGA-QH-A6X4    TCGA-QH-A6X5    TCGA-QH-A6X8 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-QH-A6X9    TCGA-QH-A6XA    TCGA-QH-A6XC    TCGA-QH-A86X    TCGA-QH-A870 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-RY-A83Y    TCGA-RY-A840    TCGA-RY-A845    TCGA-RY-A847    TCGA-S9-A6TS 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A6TU    TCGA-S9-A6TV    TCGA-S9-A6TW    TCGA-S9-A6TX    TCGA-S9-A6TY 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A6TZ    TCGA-S9-A6U0    TCGA-S9-A6U1    TCGA-S9-A6U2    TCGA-S9-A6U5 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A6U6    TCGA-S9-A6U8    TCGA-S9-A6UA    TCGA-S9-A6UB    TCGA-S9-A6WD 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A6WE    TCGA-S9-A6WG    TCGA-S9-A6WH    TCGA-S9-A6WI    TCGA-S9-A6WL 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A6WM    TCGA-S9-A6WN    TCGA-S9-A6WO    TCGA-S9-A6WP    TCGA-S9-A6WQ 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A7IQ    TCGA-S9-A7IS    TCGA-S9-A7IX    TCGA-S9-A7IY    TCGA-S9-A7IZ 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A7J0    TCGA-S9-A7J1    TCGA-S9-A7J2    TCGA-S9-A7J3    TCGA-S9-A7QW 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A7QX    TCGA-S9-A7QY    TCGA-S9-A7QZ    TCGA-S9-A7R1    TCGA-S9-A7R2 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A7R3    TCGA-S9-A7R4    TCGA-S9-A7R7    TCGA-S9-A7R8    TCGA-S9-A89V 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-S9-A89Z    TCGA-TM-A7C3    TCGA-TM-A7C4    TCGA-TM-A7C5    TCGA-TM-A7CA 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-TM-A7CF    TCGA-TM-A84B    TCGA-TM-A84C    TCGA-TM-A84F    TCGA-TM-A84G 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-TM-A84H    TCGA-TM-A84I    TCGA-TM-A84J    TCGA-TM-A84L    TCGA-TM-A84M 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-TM-A84O    TCGA-TM-A84Q    TCGA-TM-A84R    TCGA-TM-A84S    TCGA-TM-A84T 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-TQ-A7RW    TCGA-VM-A8C8    TCGA-VM-A8CA    TCGA-VM-A8CD    TCGA-VM-A8CE 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-VM-A8CH    TCGA-WY-A858    TCGA-WY-A859 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RB1 MUTATED             4                0                 1
  RB1 WILD-TYPE         171              119               178
D74V5, multiclass
                   clus
vv                  RB1 MUTATED RB1 WILD-TYPE
  ASTROCYTOMA                 4           171
  OLIGOASTROCYTOMA            0           119
  OLIGODENDROGLIOMA           1           178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
               cls
clus              0   1
  RB1 MUTATED     3   2
  RB1 WILD-TYPE  89 379
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      3    2
  RB1 WILD-TYPE   89  379
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            3            89
  YES           2           379
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     0
  RB1 WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           1     4
  RB1 WILD-TYPE                        14   434
D74V7, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  1            14
  WHITE                                      4           434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
               cls
clus              0   1
  RB1 MUTATED     0   5
  RB1 WILD-TYPE  18 415
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    5
  RB1 WILD-TYPE   18  415
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0            18
  NOT HISPANIC OR LATINO           5           415
[1] 2 2
[1] FALSE

Clustering(75) Variable = FGD6 MUTATION ANALYSIS
D75V1, survival
                sevent
clus2              0   1
  FGD6 MUTATED     2   2
  FGD6 WILD-TYPE 376  91
  FGD6 MUTATED FGD6 WILD-TYPE 
             4            467 
  FGD6 MUTATED FGD6 WILD-TYPE 
             2             91 
$`FGD6 MUTATED`
TCGA-DU-5855 TCGA-DU-6392 TCGA-DU-6396 TCGA-DU-7018 
        6.81       211.17        75.16        30.67 

$`FGD6 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         8.45       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
       15.16        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  FGD6 MUTATED FGD6 WILD-TYPE 
          6.81           0.03 
  FGD6 MUTATED FGD6 WILD-TYPE 
        211.17         182.33 
  FGD6 MUTATED FGD6 WILD-TYPE 
        52.915         18.610 
[1] "6.8 - 211.2 (52.9)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.2"
D75V2, continuous
D75V3, binary
                cls
clus               0   1
  FGD6 MUTATED     4   0
  FGD6 WILD-TYPE 203 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD6 MUTATED      4    0
  FGD6 WILD-TYPE  203  266
        clus
vv       FGD6 MUTATED FGD6 WILD-TYPE
  FEMALE            4            203
  MALE              0            266
[1] 2 2
[1] FALSE
D75V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FGD6 MUTATED             1                2                 1
  FGD6 WILD-TYPE         174              117               178
D75V5, multiclass
                   clus
vv                  FGD6 MUTATED FGD6 WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                cls
clus               0   1
  FGD6 MUTATED     3   1
  FGD6 WILD-TYPE  89 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD6 MUTATED      3    1
  FGD6 WILD-TYPE   89  380
     clus
vv    FGD6 MUTATED FGD6 WILD-TYPE
  NO             3             89
  YES            1            380
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD6 MUTATED                                  0     0
  FGD6 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD6 MUTATED                           0     4
  FGD6 WILD-TYPE                        15   434
D75V7, multiclass
                                  clus
vv                                 FGD6 MUTATED FGD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                cls
clus               0   1
  FGD6 MUTATED     0   4
  FGD6 WILD-TYPE  18 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD6 MUTATED      0    4
  FGD6 WILD-TYPE   18  416
                        clus
vv                       FGD6 MUTATED FGD6 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE

Clustering(76) Variable = CD72 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2              0   1
  CD72 MUTATED     3   0
  CD72 WILD-TYPE 375  93
  CD72 MUTATED CD72 WILD-TYPE 
             3            468 
  CD72 MUTATED CD72 WILD-TYPE 
             0             93 
$`CD72 MUTATED`
TCGA-S9-A6TZ TCGA-S9-A6WM TCGA-TM-A84I 
       28.70        19.86        28.08 

$`CD72 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  CD72 MUTATED CD72 WILD-TYPE 
         19.86           0.03 
  CD72 MUTATED CD72 WILD-TYPE 
         28.70         211.17 
  CD72 MUTATED CD72 WILD-TYPE 
         28.08          18.56 
[1] "19.9 - 28.7 (28.1)" "0.0 - 211.2 (18.6)"
[1] "hr="     "3300000"
D76V2, continuous
D76V3, binary
                cls
clus               0   1
  CD72 MUTATED     2   1
  CD72 WILD-TYPE 205 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD72 MUTATED      2    1
  CD72 WILD-TYPE  205  265
        clus
vv       CD72 MUTATED CD72 WILD-TYPE
  FEMALE            2            205
  MALE              1            265
[1] 2 2
[1] FALSE
D76V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CD72 MUTATED             3                0                 0
  CD72 WILD-TYPE         172              119               179
D76V5, multiclass
                   clus
vv                  CD72 MUTATED CD72 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                cls
clus               0   1
  CD72 MUTATED     0   3
  CD72 WILD-TYPE  92 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD72 MUTATED      0    3
  CD72 WILD-TYPE   92  378
     clus
vv    CD72 MUTATED CD72 WILD-TYPE
  NO             0             92
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD72 MUTATED                                  0     0
  CD72 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD72 MUTATED                           0     3
  CD72 WILD-TYPE                        15   435
D76V7, multiclass
                                  clus
vv                                 CD72 MUTATED CD72 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                cls
clus               0   1
  CD72 MUTATED     0   3
  CD72 WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD72 MUTATED      0    3
  CD72 WILD-TYPE   18  417
                        clus
vv                       CD72 MUTATED CD72 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(77) Variable = NKPD1 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2               0   1
  NKPD1 MUTATED     2   1
  NKPD1 WILD-TYPE 376  92
  NKPD1 MUTATED NKPD1 WILD-TYPE 
              3             468 
  NKPD1 MUTATED NKPD1 WILD-TYPE 
              1              92 
$`NKPD1 MUTATED`
TCGA-DU-7010 TCGA-HT-8010 TCGA-S9-A7R4 
       14.99         1.64        30.05 

$`NKPD1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        10.39        99.06        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  NKPD1 MUTATED NKPD1 WILD-TYPE 
           1.64            0.03 
  NKPD1 MUTATED NKPD1 WILD-TYPE 
          30.05          211.17 
  NKPD1 MUTATED NKPD1 WILD-TYPE 
          14.99           18.61 
[1] "1.6 - 30.1 (15.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "3.8"
D77V2, continuous
D77V3, binary
                 cls
clus                0   1
  NKPD1 MUTATED     2   1
  NKPD1 WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NKPD1 MUTATED      2    1
  NKPD1 WILD-TYPE  205  265
        clus
vv       NKPD1 MUTATED NKPD1 WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D77V4, continuous
[1] "Remove cluster labels:" "NKPD1 MUTATED"         
clus
  NKPD1 MUTATED NKPD1 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-HT-A61C      TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-KT-A7W1      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-P5-A5F6      TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-QH-A65V      TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-QH-A6CU      TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-QH-A6CY      TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-QH-A6X5      TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-QH-A6XC      TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-RY-A840      TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6TU      TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6TY      TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6U2      TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6UA      TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6WG      TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6WM      TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A6WQ      TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A7IY      TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A7J2      TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A7QY      TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A7R3      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" "NKPD1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NKPD1 MUTATED             2                0                 1
  NKPD1 WILD-TYPE         173              119               178
D77V5, multiclass
                   clus
vv                  NKPD1 MUTATED NKPD1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                 cls
clus                0   1
  NKPD1 MUTATED     0   3
  NKPD1 WILD-TYPE  92 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NKPD1 MUTATED      0    3
  NKPD1 WILD-TYPE   92  378
     clus
vv    NKPD1 MUTATED NKPD1 WILD-TYPE
  NO              0              92
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NKPD1 MUTATED                                  0     0
  NKPD1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NKPD1 MUTATED                           0     3
  NKPD1 WILD-TYPE                        15   435
D77V7, multiclass
                                  clus
vv                                 NKPD1 MUTATED NKPD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                 cls
clus                0   1
  NKPD1 MUTATED     1   2
  NKPD1 WILD-TYPE  17 418
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NKPD1 MUTATED      1    2
  NKPD1 WILD-TYPE   17  418
                        clus
vv                       NKPD1 MUTATED NKPD1 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             2             418
[1] 2 2
[1] FALSE

Clustering(78) Variable = MTMR1 MUTATION ANALYSIS
D78V1, survival
                 sevent
clus2               0   1
  MTMR1 MUTATED     3   1
  MTMR1 WILD-TYPE 375  92
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              4             467 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              1              92 
$`MTMR1 MUTATED`
TCGA-DU-6392 TCGA-DU-A76K TCGA-FG-A710 TCGA-S9-A7QW 
      211.17        11.41        36.66        15.06 

$`MTMR1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        7.23         5.98        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 
       15.02        16.44        22.26        28.54        10.78        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  MTMR1 MUTATED MTMR1 WILD-TYPE 
          11.41            0.03 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
         211.17          182.33 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
          25.86           18.61 
[1] "11.4 - 211.2 (25.9)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.1"
D78V2, continuous
D78V3, binary
                 cls
clus                0   1
  MTMR1 MUTATED     3   1
  MTMR1 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED      3    1
  MTMR1 WILD-TYPE  204  265
        clus
vv       MTMR1 MUTATED MTMR1 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D78V4, continuous
[1] "Remove cluster labels:" "MTMR1 MUTATED"         
clus
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-HT-A61C      TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-KT-A7W1      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-P5-A5F6      TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-QH-A65V      TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-QH-A6CU      TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-QH-A6CY      TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-QH-A6X5      TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-QH-A6XC      TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-RY-A840      TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6TU      TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6TY      TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6U2      TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6UA      TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6WG      TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6WM      TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A6WQ      TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A7IY      TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A7J2      TCGA-S9-A7J3      TCGA-S9-A7QX      TCGA-S9-A7QY 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" "MTMR1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MTMR1 MUTATED             2                0                 2
  MTMR1 WILD-TYPE         173              119               177
D78V5, multiclass
                   clus
vv                  MTMR1 MUTATED MTMR1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                 cls
clus                0   1
  MTMR1 MUTATED     1   3
  MTMR1 WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED      1    3
  MTMR1 WILD-TYPE   91  378
     clus
vv    MTMR1 MUTATED MTMR1 WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTMR1 MUTATED                                  0     0
  MTMR1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTMR1 MUTATED                           0     4
  MTMR1 WILD-TYPE                        15   434
D78V7, multiclass
                                  clus
vv                                 MTMR1 MUTATED MTMR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                 cls
clus                0   1
  MTMR1 MUTATED     0   4
  MTMR1 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED      0    4
  MTMR1 WILD-TYPE   18  416
                        clus
vv                       MTMR1 MUTATED MTMR1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(79) Variable = GPR133 MUTATION ANALYSIS
D79V1, survival
                  sevent
clus2                0   1
  GPR133 MUTATED     3   0
  GPR133 WILD-TYPE 375  93
  GPR133 MUTATED GPR133 WILD-TYPE 
               3              468 
  GPR133 MUTATED GPR133 WILD-TYPE 
               0               93 
$`GPR133 MUTATED`
TCGA-DU-6392 TCGA-FG-A4MY TCGA-W9-A837 
      211.17        23.70        51.06 

$`GPR133 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21         8.05        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  GPR133 MUTATED GPR133 WILD-TYPE 
           23.70             0.03 
  GPR133 MUTATED GPR133 WILD-TYPE 
          211.17           182.33 
  GPR133 MUTATED GPR133 WILD-TYPE 
           51.06            18.56 
[1] "23.7 - 211.2 (51.1)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D79V2, continuous
[1] "Remove cluster labels:" "GPR133 MUTATED"        
clus
  GPR133 MUTATED GPR133 WILD-TYPE 
               2              470 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5394 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-CS-5395       TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-CS-6188       TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-CS-6667       TCGA-CS-6668       TCGA-CS-6669       TCGA-CS-6670 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-5270       TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5275 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278       TCGA-DB-5279 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DB-A4X9       TCGA-DB-A4XA 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A4XB       TCGA-DB-A4XC       TCGA-DB-A4XD       TCGA-DB-A4XE 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A4XF       TCGA-DB-A4XG       TCGA-DB-A4XH       TCGA-DB-A64L 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A64O       TCGA-DB-A64P       TCGA-DB-A64Q       TCGA-DB-A64R 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A64S       TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A64X       TCGA-DB-A75K       TCGA-DB-A75L       TCGA-DB-A75M 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DB-A75O       TCGA-DB-A75P       TCGA-DH-5140       TCGA-DH-5141 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A669 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DH-A66B       TCGA-DH-A66D       TCGA-DH-A66F       TCGA-DH-A66G 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DH-A7UR       TCGA-DH-A7US       TCGA-DH-A7UT       TCGA-DH-A7UU 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5847       TCGA-DU-5849       TCGA-DU-5851 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-5852       TCGA-DU-5853       TCGA-DU-5854       TCGA-DU-5855 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-5870       TCGA-DU-5871       TCGA-DU-5872       TCGA-DU-5874 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-6393       TCGA-DU-6394       TCGA-DU-6395       TCGA-DU-6396 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-6397       TCGA-DU-6399       TCGA-DU-6400       TCGA-DU-6401 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-6402       TCGA-DU-6403       TCGA-DU-6404       TCGA-DU-6405 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-6406       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-6542       TCGA-DU-7006       TCGA-DU-7007       TCGA-DU-7008 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-7009       TCGA-DU-7010       TCGA-DU-7011       TCGA-DU-7012 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-7290       TCGA-DU-7292       TCGA-DU-7294       TCGA-DU-7298 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-7299       TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-7304       TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-8161       TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8164 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-8165       TCGA-DU-8166       TCGA-DU-8167       TCGA-DU-8168 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TT 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A5TY       TCGA-DU-A6S2 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A6S3       TCGA-DU-A6S6       TCGA-DU-A6S7       TCGA-DU-A6S8 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A76K       TCGA-DU-A76L       TCGA-DU-A76O       TCGA-DU-A76R 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A7T6       TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-DU-A7TC       TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-DU-A7TJ 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5305 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5319 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-E1-5322       TCGA-E1-A7YO       TCGA-E1-A7YV       TCGA-E1-A7YW 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-E1-A7Z6       TCGA-EZ-7264       TCGA-F6-A8O3       TCGA-F6-A8O4 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-5962       TCGA-FG-5963       TCGA-FG-5964       TCGA-FG-5965 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-6692       TCGA-FG-7634       TCGA-FG-7636       TCGA-FG-7637 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-7638       TCGA-FG-7641       TCGA-FG-7643       TCGA-FG-8181 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-8182       TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-8188       TCGA-FG-8189       TCGA-FG-8191       TCGA-FG-A4MT 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-A4MU       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-A60K       TCGA-FG-A60L       TCGA-FG-A6IZ       TCGA-FG-A6J1 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-A6J3       TCGA-FG-A70Y       TCGA-FG-A70Z       TCGA-FG-A710 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A713       TCGA-FG-A87N       TCGA-FG-A87Q 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-FN-7833       TCGA-HT-7467       TCGA-HT-7468       TCGA-HT-7469 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7471       TCGA-HT-7472       TCGA-HT-7473 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7474       TCGA-HT-7475       TCGA-HT-7476       TCGA-HT-7477 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7478       TCGA-HT-7479       TCGA-HT-7480       TCGA-HT-7481 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7482       TCGA-HT-7483       TCGA-HT-7485       TCGA-HT-7601 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7602       TCGA-HT-7603       TCGA-HT-7604       TCGA-HT-7605 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7606       TCGA-HT-7607       TCGA-HT-7608       TCGA-HT-7609 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7610       TCGA-HT-7611       TCGA-HT-7616       TCGA-HT-7620 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7676       TCGA-HT-7677       TCGA-HT-7680       TCGA-HT-7681 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7684       TCGA-HT-7686       TCGA-HT-7687       TCGA-HT-7688 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7689       TCGA-HT-7690       TCGA-HT-7691       TCGA-HT-7692 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7695       TCGA-HT-7854 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7855       TCGA-HT-7856       TCGA-HT-7857       TCGA-HT-7858 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7860       TCGA-HT-7873       TCGA-HT-7874       TCGA-HT-7875 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7877       TCGA-HT-7879       TCGA-HT-7880       TCGA-HT-7881 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-7882       TCGA-HT-7884       TCGA-HT-7902       TCGA-HT-8010 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-8011       TCGA-HT-8012       TCGA-HT-8013       TCGA-HT-8015 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-8018       TCGA-HT-8019       TCGA-HT-8104       TCGA-HT-8105 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-8106       TCGA-HT-8107       TCGA-HT-8108       TCGA-HT-8109 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-8110       TCGA-HT-8111       TCGA-HT-8113       TCGA-HT-8114 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-8558       TCGA-HT-8563       TCGA-HT-8564       TCGA-HT-A4DS 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A4DV       TCGA-HT-A5R5       TCGA-HT-A5R7       TCGA-HT-A5R9 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RB       TCGA-HT-A5RC       TCGA-HT-A614 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A615       TCGA-HT-A616       TCGA-HT-A617       TCGA-HT-A618 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A619       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A74H       TCGA-HT-A74J       TCGA-HT-A74K       TCGA-HT-A74L 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HT-A74O       TCGA-HW-7486       TCGA-HW-7487       TCGA-HW-7489 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HW-7490       TCGA-HW-7491       TCGA-HW-7495       TCGA-HW-8319 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HW-8320       TCGA-HW-8321       TCGA-HW-8322       TCGA-HW-A5KJ 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-HW-A5KK       TCGA-HW-A5KL       TCGA-HW-A5KM       TCGA-IK-7675 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-IK-8125       TCGA-KT-A74X       TCGA-KT-A7W1       TCGA-P5-A5ET 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-P5-A5EY       TCGA-P5-A5EZ       TCGA-P5-A5F0       TCGA-P5-A5F1 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6       TCGA-P5-A72U 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-P5-A72W       TCGA-P5-A72X       TCGA-P5-A72Z       TCGA-P5-A730 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-P5-A731       TCGA-P5-A733       TCGA-QH-A65R       TCGA-QH-A65S 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-QH-A65V       TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-QH-A6CU       TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-QH-A6CY       TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-QH-A6X5       TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-QH-A6XC       TCGA-QH-A86X       TCGA-QH-A870       TCGA-R8-A6MK 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-R8-A6ML       TCGA-R8-A6MO       TCGA-R8-A73M       TCGA-RY-A83X 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-RY-A83Y       TCGA-RY-A83Z       TCGA-RY-A840       TCGA-RY-A843 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6U9 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6UA       TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6WG       TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6WM       TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A6WQ       TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A7IY       TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A7J2       TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A7QY       TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A7R3       TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-S9-A89V       TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-TM-A7C5       TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-TM-A84C       TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-TM-A84I       TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-TM-A84O       TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-TM-A84T       TCGA-TQ-A7RH       TCGA-TQ-A7RW       TCGA-VM-A8C8 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-VM-A8C9       TCGA-VM-A8CA       TCGA-VM-A8CB       TCGA-VM-A8CD 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-VV-A829       TCGA-VV-A86M 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-VW-A7QS       TCGA-VW-A8FI       TCGA-WH-A86K       TCGA-WY-A858 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-WY-A859       TCGA-WY-A85A       TCGA-WY-A85B       TCGA-WY-A85C 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
      TCGA-WY-A85D       TCGA-WY-A85E 
"GPR133 WILD-TYPE" "GPR133 WILD-TYPE" 
D79V3, binary
                  cls
clus                 0   1
  GPR133 MUTATED     2   1
  GPR133 WILD-TYPE 205 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR133 MUTATED      2    1
  GPR133 WILD-TYPE  205  265
        clus
vv       GPR133 MUTATED GPR133 WILD-TYPE
  FEMALE              2              205
  MALE                1              265
[1] 2 2
[1] FALSE
D79V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  GPR133 MUTATED             1                1                 1
  GPR133 WILD-TYPE         174              118               178
D79V5, multiclass
                   clus
vv                  GPR133 MUTATED GPR133 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                  cls
clus                 0   1
  GPR133 MUTATED     1   2
  GPR133 WILD-TYPE  91 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR133 MUTATED      1    2
  GPR133 WILD-TYPE   91  379
     clus
vv    GPR133 MUTATED GPR133 WILD-TYPE
  NO               1               91
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR133 MUTATED                                  0     0
  GPR133 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR133 MUTATED                           0     3
  GPR133 WILD-TYPE                        15   435
D79V7, multiclass
                                  clus
vv                                 GPR133 MUTATED GPR133 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                  cls
clus                 0   1
  GPR133 MUTATED     1   2
  GPR133 WILD-TYPE  17 418
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR133 MUTATED      1    2
  GPR133 WILD-TYPE   17  418
                        clus
vv                       GPR133 MUTATED GPR133 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              2              418
[1] 2 2
[1] FALSE

Clustering(80) Variable = CNOT4 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  CNOT4 MUTATED     5   0
  CNOT4 WILD-TYPE 373  93
  CNOT4 MUTATED CNOT4 WILD-TYPE 
              5             466 
  CNOT4 MUTATED CNOT4 WILD-TYPE 
              0              93 
$`CNOT4 MUTATED`
TCGA-DU-6392 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-FG-A713 TCGA-S9-A6TW 
      211.17        14.24        12.59        20.45        37.84 

$`CNOT4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        14.17        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        18.77        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  CNOT4 MUTATED CNOT4 WILD-TYPE 
          12.59            0.03 
  CNOT4 MUTATED CNOT4 WILD-TYPE 
         211.17          182.33 
  CNOT4 MUTATED CNOT4 WILD-TYPE 
          20.45           18.61 
[1] "12.6 - 211.2 (20.4)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D80V2, continuous
D80V3, binary
                 cls
clus                0   1
  CNOT4 MUTATED     2   3
  CNOT4 WILD-TYPE 205 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT4 MUTATED      2    3
  CNOT4 WILD-TYPE  205  263
        clus
vv       CNOT4 MUTATED CNOT4 WILD-TYPE
  FEMALE             2             205
  MALE               3             263
[1] 2 2
[1] FALSE
D80V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CNOT4 MUTATED             2                2                 1
  CNOT4 WILD-TYPE         173              117               178
D80V5, multiclass
                   clus
vv                  CNOT4 MUTATED CNOT4 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                 cls
clus                0   1
  CNOT4 MUTATED     1   4
  CNOT4 WILD-TYPE  91 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT4 MUTATED      1    4
  CNOT4 WILD-TYPE   91  377
     clus
vv    CNOT4 MUTATED CNOT4 WILD-TYPE
  NO              1              91
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNOT4 MUTATED                                  0     0
  CNOT4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNOT4 MUTATED                           0     5
  CNOT4 WILD-TYPE                        15   433
D80V7, multiclass
                                  clus
vv                                 CNOT4 MUTATED CNOT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, binary
                 cls
clus                0   1
  CNOT4 MUTATED     0   5
  CNOT4 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT4 MUTATED      0    5
  CNOT4 WILD-TYPE   18  415
                        clus
vv                       CNOT4 MUTATED CNOT4 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(81) Variable = ZBTB20 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    16   2
  ZBTB20 WILD-TYPE 362  91
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              18              453 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               2               91 
$`ZBTB20 MUTATED`
TCGA-DB-A4XH TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-6392 
       31.63        29.23        14.40        13.12        14.56       211.17 
TCGA-DU-6408 TCGA-FG-8187 TCGA-FG-A6J1 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7881 
      114.08        20.09        16.44         4.57        22.06        35.47 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HW-A5KJ TCGA-QH-A65R TCGA-RY-A847 TCGA-S9-A6WL 
       28.27        15.72        20.35        15.16        30.67        31.10 

$`ZBTB20 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       31.40        27.45        27.81        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        13.38         3.45        18.61        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 
       23.18       122.47        17.29         3.16        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        13.74         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KK 
        4.31        21.70        21.60        19.59        17.82        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S 
       13.25        11.64         0.20         9.01        13.61         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS 
        5.46         9.90        28.08         2.07        19.59        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
            4.57             0.03 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          211.17           182.33 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          21.205           18.510 
[1] "4.6 - 211.2 (21.2)" "0.0 - 182.3 (18.5)"
[1] "hr=" "2.4"
D81V2, continuous
D81V3, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     7  12
  ZBTB20 WILD-TYPE 200 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      7   12
  ZBTB20 WILD-TYPE  200  254
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE              7              200
  MALE               12              254
[1] 2 2
[1] FALSE
D81V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZBTB20 MUTATED             4                4                11
  ZBTB20 WILD-TYPE         171              115               168
D81V5, multiclass
                   clus
vv                  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASTROCYTOMA                    4              171
  OLIGOASTROCYTOMA               4              115
  OLIGODENDROGLIOMA             11              168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     2  17
  ZBTB20 WILD-TYPE  90 364
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      2   17
  ZBTB20 WILD-TYPE   90  364
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO               2               90
  YES             17              364
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB20 MUTATED                                  0     0
  ZBTB20 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB20 MUTATED                           2    17
  ZBTB20 WILD-TYPE                        13   421
D81V7, multiclass
                                  clus
vv                                 ZBTB20 MUTATED ZBTB20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     2               13
  WHITE                                        17              421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     1  17
  ZBTB20 WILD-TYPE  17 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      1   17
  ZBTB20 WILD-TYPE   17  403
                        clus
vv                       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             17              403
[1] 2 2
[1] FALSE

Clustering(82) Variable = ROBO3 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  ROBO3 MUTATED     4   0
  ROBO3 WILD-TYPE 374  93
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             467 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              0              93 
$`ROBO3 MUTATED`
TCGA-CS-6667 TCGA-DB-A64L TCGA-HT-7676 TCGA-P5-A5F2 
        7.56        24.20         0.16         7.63 

$`ROBO3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  ROBO3 MUTATED ROBO3 WILD-TYPE 
           0.16            0.03 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
          24.20          211.17 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
          7.595          18.610 
[1] "0.2 - 24.2 (7.6)"   "0.0 - 211.2 (18.6)"
[1] "hr="     "1200000"
D82V2, continuous
D82V3, binary
                 cls
clus                0   1
  ROBO3 MUTATED     3   1
  ROBO3 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      3    1
  ROBO3 WILD-TYPE  204  265
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D82V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ROBO3 MUTATED             2                0                 2
  ROBO3 WILD-TYPE         173              119               177
D82V5, multiclass
                   clus
vv                  ROBO3 MUTATED ROBO3 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                 cls
clus                0   1
  ROBO3 MUTATED     1   3
  ROBO3 WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      1    3
  ROBO3 WILD-TYPE   91  378
     clus
vv    ROBO3 MUTATED ROBO3 WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROBO3 MUTATED                                  0     0
  ROBO3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ROBO3 MUTATED                           0     4
  ROBO3 WILD-TYPE                        15   434
D82V7, multiclass
                                  clus
vv                                 ROBO3 MUTATED ROBO3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V8, binary
                 cls
clus                0   1
  ROBO3 MUTATED     0   4
  ROBO3 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      0    4
  ROBO3 WILD-TYPE   18  416
                        clus
vv                       ROBO3 MUTATED ROBO3 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(83) Variable = PDE8A MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  PDE8A MUTATED     3   3
  PDE8A WILD-TYPE 375  90
  PDE8A MUTATED PDE8A WILD-TYPE 
              6             465 
  PDE8A MUTATED PDE8A WILD-TYPE 
              3              90 
$`PDE8A MUTATED`
TCGA-DU-6392 TCGA-DU-7018 TCGA-DU-8158 TCGA-DU-A76L TCGA-HT-7688 TCGA-WH-A86K 
      211.17        30.67         5.10        26.76        31.69        13.32 

$`PDE8A WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54         8.84        90.77        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  PDE8A MUTATED PDE8A WILD-TYPE 
           5.10            0.03 
  PDE8A MUTATED PDE8A WILD-TYPE 
         211.17          182.33 
  PDE8A MUTATED PDE8A WILD-TYPE 
         28.715          18.610 
[1] "5.1 - 211.2 (28.7)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.3"
D83V2, continuous
D83V3, binary
                 cls
clus                0   1
  PDE8A MUTATED     3   3
  PDE8A WILD-TYPE 204 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      3    3
  PDE8A WILD-TYPE  204  263
        clus
vv       PDE8A MUTATED PDE8A WILD-TYPE
  FEMALE             3             204
  MALE               3             263
[1] 2 2
[1] FALSE
D83V4, continuous
[1] "Remove cluster labels:" "PDE8A MUTATED"         
clus
  PDE8A MUTATED PDE8A WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7019 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8161      TCGA-DU-8162      TCGA-DU-8163 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168      TCGA-DU-A5TP 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU      TCGA-DU-A5TW 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7      TCGA-DU-A6S8 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8      TCGA-DU-A7TA 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD      TCGA-DU-A7TG 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5305 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318      TCGA-E1-5319 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV      TCGA-E1-A7YW 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965      TCGA-FG-6688 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691      TCGA-FG-7636 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185      TCGA-FG-8186 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189      TCGA-FG-A4MT 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J      TCGA-FG-A60L 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711      TCGA-FG-A713 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470      TCGA-HT-7475 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607      TCGA-HT-7609 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692      TCGA-HT-7693 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875      TCGA-HT-7884 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7      TCGA-HT-A5RA 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C      TCGA-HT-A74L 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1      TCGA-P5-A5EU 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PDE8A MUTATED             3                0                 3
  PDE8A WILD-TYPE         172              119               176
D83V5, multiclass
                   clus
vv                  PDE8A MUTATED PDE8A WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                 cls
clus                0   1
  PDE8A MUTATED     2   4
  PDE8A WILD-TYPE  90 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      2    4
  PDE8A WILD-TYPE   90  377
     clus
vv    PDE8A MUTATED PDE8A WILD-TYPE
  NO              2              90
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDE8A MUTATED                                  0     0
  PDE8A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDE8A MUTATED                           0     6
  PDE8A WILD-TYPE                        15   432
D83V7, multiclass
                                  clus
vv                                 PDE8A MUTATED PDE8A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V8, binary
                 cls
clus                0   1
  PDE8A MUTATED     0   6
  PDE8A WILD-TYPE  18 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      0    6
  PDE8A WILD-TYPE   18  414
                        clus
vv                       PDE8A MUTATED PDE8A WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             414
[1] 2 2
[1] FALSE

Clustering(84) Variable = EEF1D MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2               0   1
  EEF1D MUTATED     2   1
  EEF1D WILD-TYPE 376  92
  EEF1D MUTATED EEF1D WILD-TYPE 
              3             468 
  EEF1D MUTATED EEF1D WILD-TYPE 
              1              92 
$`EEF1D MUTATED`
TCGA-DU-6392 TCGA-DU-6396 TCGA-HT-7603 
      211.17        75.16        23.18 

$`EEF1D WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  EEF1D MUTATED EEF1D WILD-TYPE 
          23.18            0.03 
  EEF1D MUTATED EEF1D WILD-TYPE 
         211.17          182.33 
  EEF1D MUTATED EEF1D WILD-TYPE 
          75.16           18.56 
[1] "23.2 - 211.2 (75.2)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.5"
D84V2, continuous
D84V3, binary
                 cls
clus                0   1
  EEF1D MUTATED     2   1
  EEF1D WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      2    1
  EEF1D WILD-TYPE  205  265
        clus
vv       EEF1D MUTATED EEF1D WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D84V4, continuous
[1] "Remove cluster labels:" "EEF1D MUTATED"         
clus
  EEF1D MUTATED EEF1D WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" "EEF1D WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EEF1D MUTATED             1                1                 1
  EEF1D WILD-TYPE         174              118               178
D84V5, multiclass
                   clus
vv                  EEF1D MUTATED EEF1D WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                 cls
clus                0   1
  EEF1D MUTATED     3   0
  EEF1D WILD-TYPE  89 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      3    0
  EEF1D WILD-TYPE   89  381
     clus
vv    EEF1D MUTATED EEF1D WILD-TYPE
  NO              3              89
  YES             0             381
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1D MUTATED                                  0     0
  EEF1D WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EEF1D MUTATED                           0     3
  EEF1D WILD-TYPE                        15   435
D84V7, multiclass
                                  clus
vv                                 EEF1D MUTATED EEF1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V8, binary
                 cls
clus                0   1
  EEF1D MUTATED     0   3
  EEF1D WILD-TYPE  18 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      0    3
  EEF1D WILD-TYPE   18  417
                        clus
vv                       EEF1D MUTATED EEF1D WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(85) Variable = MET MUTATION ANALYSIS
D85V1, survival
               sevent
clus2             0   1
  MET MUTATED     6   1
  MET WILD-TYPE 372  92
  MET MUTATED MET WILD-TYPE 
            7           464 
  MET MUTATED MET WILD-TYPE 
            1            92 
$`MET MUTATED`
TCGA-DU-6392 TCGA-FG-6689 TCGA-HT-7471 TCGA-HT-7482 TCGA-HT-A61C TCGA-QH-A6CW 
      211.17        14.93         0.13       106.95        17.65        13.61 
TCGA-S9-A6WP 
       15.16 

$`MET WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 
       47.77        25.48        34.36        36.82        18.77        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54        40.11         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       95.93       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A74H 
       16.14        16.83        21.40         6.38        17.52         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
       15.85        14.04        19.33        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ 
       84.99        31.10        19.86        15.91        18.61        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  MET MUTATED MET WILD-TYPE 
         0.13          0.03 
  MET MUTATED MET WILD-TYPE 
       211.17        182.33 
  MET MUTATED MET WILD-TYPE 
        15.16         18.66 
[1] "0.1 - 211.2 (15.2)" "0.0 - 182.3 (18.7)"
[1] "hr=" "3"  
D85V2, continuous
D85V3, binary
               cls
clus              0   1
  MET MUTATED     3   4
  MET WILD-TYPE 204 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      3    4
  MET WILD-TYPE  204  262
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           3           204
  MALE             4           262
[1] 2 2
[1] FALSE
D85V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MET MUTATED             2                3                 2
  MET WILD-TYPE         173              116               177
D85V5, multiclass
                   clus
vv                  MET MUTATED MET WILD-TYPE
  ASTROCYTOMA                 2           173
  OLIGOASTROCYTOMA            3           116
  OLIGODENDROGLIOMA           2           177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
               cls
clus              0   1
  MET MUTATED     3   4
  MET WILD-TYPE  89 377
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      3    4
  MET WILD-TYPE   89  377
     clus
vv    MET MUTATED MET WILD-TYPE
  NO            3            89
  YES           4           377
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           0     7
  MET WILD-TYPE                        15   431
D85V7, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                      7           431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V8, binary
               cls
clus              0   1
  MET MUTATED     0   7
  MET WILD-TYPE  18 413
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      0    7
  MET WILD-TYPE   18  413
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               0            18
  NOT HISPANIC OR LATINO           7           413
[1] 2 2
[1] FALSE

Clustering(86) Variable = CUL4B MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2               0   1
  CUL4B MUTATED     9   1
  CUL4B WILD-TYPE 369  92
  CUL4B MUTATED CUL4B WILD-TYPE 
             10             461 
  CUL4B MUTATED CUL4B WILD-TYPE 
              1              92 
$`CUL4B MUTATED`
TCGA-CS-6670 TCGA-DU-6392 TCGA-FG-A4MW TCGA-FG-A87N TCGA-HT-A615 TCGA-HT-A61B 
        6.61       211.17        18.38        13.58        16.93        17.52 
TCGA-QH-A65R TCGA-S9-A6TZ TCGA-S9-A6WM TCGA-S9-A6WN 
       15.16        28.70        19.86        15.91 

$`CUL4B WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40         6.38        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        9.01        13.61         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       37.84        34.49        31.33        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  CUL4B MUTATED CUL4B WILD-TYPE 
           6.61            0.03 
  CUL4B MUTATED CUL4B WILD-TYPE 
         211.17          182.33 
  CUL4B MUTATED CUL4B WILD-TYPE 
         17.225          18.710 
[1] "6.6 - 211.2 (17.2)" "0.0 - 182.3 (18.7)"
[1] "hr=" "2.5"
D86V2, continuous
D86V3, binary
                 cls
clus                0   1
  CUL4B MUTATED     7   3
  CUL4B WILD-TYPE 200 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      7    3
  CUL4B WILD-TYPE  200  263
        clus
vv       CUL4B MUTATED CUL4B WILD-TYPE
  FEMALE             7             200
  MALE               3             263
[1] 2 2
[1] FALSE
D86V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CUL4B MUTATED             6                1                 3
  CUL4B WILD-TYPE         169              118               176
D86V5, multiclass
                   clus
vv                  CUL4B MUTATED CUL4B WILD-TYPE
  ASTROCYTOMA                   6             169
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                 cls
clus                0   1
  CUL4B MUTATED     2   8
  CUL4B WILD-TYPE  90 373
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      2    8
  CUL4B WILD-TYPE   90  373
     clus
vv    CUL4B MUTATED CUL4B WILD-TYPE
  NO              2              90
  YES             8             373
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL4B MUTATED                                  0     1
  CUL4B WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CUL4B MUTATED                           0     9
  CUL4B WILD-TYPE                        15   429
D86V7, multiclass
                                  clus
vv                                 CUL4B MUTATED CUL4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               7
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        9             429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V8, binary
                 cls
clus                0   1
  CUL4B MUTATED     0  10
  CUL4B WILD-TYPE  18 410
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      0   10
  CUL4B WILD-TYPE   18  410
                        clus
vv                       CUL4B MUTATED CUL4B WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            10             410
[1] 2 2
[1] FALSE

Clustering(87) Variable = SNX31 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  SNX31 MUTATED     4   0
  SNX31 WILD-TYPE 374  93
  SNX31 MUTATED SNX31 WILD-TYPE 
              4             467 
  SNX31 MUTATED SNX31 WILD-TYPE 
              0              93 
$`SNX31 MUTATED`
TCGA-DB-A4XH TCGA-DU-6392 TCGA-P5-A72U TCGA-S9-A6U9 
       31.63       211.17         0.16        95.93 

$`SNX31 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         1.28        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       16.08        98.24         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  SNX31 MUTATED SNX31 WILD-TYPE 
           0.16            0.03 
  SNX31 MUTATED SNX31 WILD-TYPE 
         211.17          182.33 
  SNX31 MUTATED SNX31 WILD-TYPE 
          63.78           18.61 
[1] "0.2 - 211.2 (63.8)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D87V2, continuous
D87V3, binary
                 cls
clus                0   1
  SNX31 MUTATED     3   1
  SNX31 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX31 MUTATED      3    1
  SNX31 WILD-TYPE  204  265
        clus
vv       SNX31 MUTATED SNX31 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D87V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SNX31 MUTATED             2                1                 1
  SNX31 WILD-TYPE         173              118               178
D87V5, multiclass
                   clus
vv                  SNX31 MUTATED SNX31 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                 cls
clus                0   1
  SNX31 MUTATED     1   3
  SNX31 WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX31 MUTATED      1    3
  SNX31 WILD-TYPE   91  378
     clus
vv    SNX31 MUTATED SNX31 WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNX31 MUTATED                                  0     0
  SNX31 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SNX31 MUTATED                           0     4
  SNX31 WILD-TYPE                        15   434
D87V7, multiclass
                                  clus
vv                                 SNX31 MUTATED SNX31 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V8, binary
                 cls
clus                0   1
  SNX31 MUTATED     0   4
  SNX31 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX31 MUTATED      0    4
  SNX31 WILD-TYPE   18  416
                        clus
vv                       SNX31 MUTATED SNX31 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(88) Variable = PHF3 MUTATION ANALYSIS
D88V1, survival
                sevent
clus2              0   1
  PHF3 MUTATED     5   3
  PHF3 WILD-TYPE 373  90
  PHF3 MUTATED PHF3 WILD-TYPE 
             8            463 
  PHF3 MUTATED PHF3 WILD-TYPE 
             3             90 
$`PHF3 MUTATED`
TCGA-CS-5395 TCGA-DB-A64O TCGA-DU-6392 TCGA-E1-5304 TCGA-FG-8186 TCGA-HT-A74K 
       21.01        25.48       211.17        41.13        16.01        15.35 
TCGA-QH-A870 TCGA-S9-A6U9 
       12.99        95.93 

$`PHF3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        24.20        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        14.24        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
        1.91        16.50         5.03        11.08        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB 
       23.64        32.61        16.08        98.24         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  PHF3 MUTATED PHF3 WILD-TYPE 
         12.99           0.03 
  PHF3 MUTATED PHF3 WILD-TYPE 
        211.17         182.33 
  PHF3 MUTATED PHF3 WILD-TYPE 
        23.245         18.610 
[1] "13.0 - 211.2 (23.2)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "1.1"
D88V2, continuous
D88V3, binary
                cls
clus               0   1
  PHF3 MUTATED     4   4
  PHF3 WILD-TYPE 203 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED      4    4
  PHF3 WILD-TYPE  203  262
        clus
vv       PHF3 MUTATED PHF3 WILD-TYPE
  FEMALE            4            203
  MALE              4            262
[1] 2 2
[1] FALSE
D88V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PHF3 MUTATED             3                3                 2
  PHF3 WILD-TYPE         172              116               177
D88V5, multiclass
                   clus
vv                  PHF3 MUTATED PHF3 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V6, binary
                cls
clus               0   1
  PHF3 MUTATED     3   5
  PHF3 WILD-TYPE  89 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED      3    5
  PHF3 WILD-TYPE   89  376
     clus
vv    PHF3 MUTATED PHF3 WILD-TYPE
  NO             3             89
  YES            5            376
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF3 MUTATED                                  0     0
  PHF3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHF3 MUTATED                           1     7
  PHF3 WILD-TYPE                        14   431
D88V7, multiclass
                                  clus
vv                                 PHF3 MUTATED PHF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   1             14
  WHITE                                       7            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V8, binary
                cls
clus               0   1
  PHF3 MUTATED     1   6
  PHF3 WILD-TYPE  17 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED      1    6
  PHF3 WILD-TYPE   17  414
                        clus
vv                       PHF3 MUTATED PHF3 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            6            414
[1] 2 2
[1] FALSE

Clustering(89) Variable = G6PC MUTATION ANALYSIS
D89V1, survival
                sevent
clus2              0   1
  G6PC MUTATED     3   2
  G6PC WILD-TYPE 375  91
  G6PC MUTATED G6PC WILD-TYPE 
             5            466 
  G6PC MUTATED G6PC WILD-TYPE 
             2             91 
$`G6PC MUTATED`
TCGA-DU-6392 TCGA-DU-7292 TCGA-HT-8105 TCGA-HT-A74H TCGA-IK-7675 
      211.17         7.96         6.25         2.43        19.00 

$`G6PC WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
       17.65        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  G6PC MUTATED G6PC WILD-TYPE 
          2.43           0.03 
  G6PC MUTATED G6PC WILD-TYPE 
        211.17         182.33 
  G6PC MUTATED G6PC WILD-TYPE 
          7.96          18.61 
[1] "2.4 - 211.2 (8.0)"  "0.0 - 182.3 (18.6)"
[1] "hr=" "1.1"
D89V2, continuous
D89V3, binary
                cls
clus               0   1
  G6PC MUTATED     1   4
  G6PC WILD-TYPE 206 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  G6PC MUTATED      1    4
  G6PC WILD-TYPE  206  262
        clus
vv       G6PC MUTATED G6PC WILD-TYPE
  FEMALE            1            206
  MALE              4            262
[1] 2 2
[1] FALSE
D89V4, continuous
[1] "Remove cluster labels:" "G6PC MUTATED"          
clus
  G6PC MUTATED G6PC WILD-TYPE 
             1            268 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-8168     TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-A5TU     TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-A6S7     TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-A7T8     TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-DU-A7TD     TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-E1-5304     TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-E1-A7YV     TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-5965     TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-6691     TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-8185     TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-8189     TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-A60J     TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-FG-A711     TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-7470     TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-7607     TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-7692     TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-7875     TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-A5R7     TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-A617     TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-HT-A61C     TCGA-HT-A74L     TCGA-KT-A74X     TCGA-KT-A7W1 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6TZ     TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6U5     TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6UB     TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6WH     TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A6WN     TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A7IQ     TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A7IZ     TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A7J3     TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A7QZ     TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A7R4     TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-S9-A89Z     TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-TM-A7CA     TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-TM-A84F     TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-TM-A84J     TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-TM-A84Q     TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-TQ-A7RW     TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
    TCGA-VM-A8CE     TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" "G6PC WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  G6PC MUTATED             3                0                 2
  G6PC WILD-TYPE         172              119               177
D89V5, multiclass
                   clus
vv                  G6PC MUTATED G6PC WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V6, binary
                cls
clus               0   1
  G6PC MUTATED     2   3
  G6PC WILD-TYPE  90 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  G6PC MUTATED      2    3
  G6PC WILD-TYPE   90  378
     clus
vv    G6PC MUTATED G6PC WILD-TYPE
  NO             2             90
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G6PC MUTATED                                  0     0
  G6PC WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  G6PC MUTATED                           0     5
  G6PC WILD-TYPE                        15   433
D89V7, multiclass
                                  clus
vv                                 G6PC MUTATED G6PC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V8, binary
                cls
clus               0   1
  G6PC MUTATED     1   4
  G6PC WILD-TYPE  17 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  G6PC MUTATED      1    4
  G6PC WILD-TYPE   17  416
                        clus
vv                       G6PC MUTATED G6PC WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE

Clustering(90) Variable = FOXQ1 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 376  92
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             468 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1              92 
$`FOXQ1 MUTATED`
TCGA-DU-6392 TCGA-DU-8162 TCGA-HT-7688 
      211.17        14.60        31.69 

$`FOXQ1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          14.60            0.03 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
         211.17          182.33 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          31.69           18.61 
[1] "14.6 - 211.2 (31.7)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2"  
D90V2, continuous
D90V3, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  205  265
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D90V4, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FOXQ1 MUTATED             1                1                 1
  FOXQ1 WILD-TYPE         174              118               178
D90V5, multiclass
                   clus
vv                  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE  90 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE   90  380
     clus
vv    FOXQ1 MUTATED FOXQ1 WILD-TYPE
  NO              2              90
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXQ1 MUTATED                                  0     0
  FOXQ1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXQ1 MUTATED                           0     3
  FOXQ1 WILD-TYPE                        15   435
D90V7, multiclass
                                  clus
vv                                 FOXQ1 MUTATED FOXQ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V8, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0   3
  FOXQ1 WILD-TYPE  18 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0    3
  FOXQ1 WILD-TYPE   18  417
                        clus
vv                       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(91) Variable = AEBP1 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2               0   1
  AEBP1 MUTATED     2   1
  AEBP1 WILD-TYPE 376  92
  AEBP1 MUTATED AEBP1 WILD-TYPE 
              3             468 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
              1              92 
$`AEBP1 MUTATED`
TCGA-DU-7300 TCGA-HT-8107 TCGA-HW-7495 
       62.01         0.46         4.31 

$`AEBP1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  AEBP1 MUTATED AEBP1 WILD-TYPE 
           0.46            0.03 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
          62.01          211.17 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
           4.31           18.61 
[1] "0.5 - 62.0 (4.3)"   "0.0 - 211.2 (18.6)"
[1] "hr=" "2.2"
D91V2, continuous
D91V3, binary
                 cls
clus                0   1
  AEBP1 MUTATED     2   2
  AEBP1 WILD-TYPE 205 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      2    2
  AEBP1 WILD-TYPE  205  264
        clus
vv       AEBP1 MUTATED AEBP1 WILD-TYPE
  FEMALE             2             205
  MALE               2             264
[1] 2 2
[1] FALSE
D91V4, continuous
[1] "Remove cluster labels:" "AEBP1 MUTATED"         
clus
  AEBP1 MUTATED AEBP1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" "AEBP1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AEBP1 MUTATED             1                0                 3
  AEBP1 WILD-TYPE         174              119               176
D91V5, multiclass
                   clus
vv                  AEBP1 MUTATED AEBP1 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V6, binary
                 cls
clus                0   1
  AEBP1 MUTATED     0   4
  AEBP1 WILD-TYPE  92 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      0    4
  AEBP1 WILD-TYPE   92  377
     clus
vv    AEBP1 MUTATED AEBP1 WILD-TYPE
  NO              0              92
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AEBP1 MUTATED                                  0     0
  AEBP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AEBP1 MUTATED                           0     4
  AEBP1 WILD-TYPE                        15   434
D91V7, multiclass
                                  clus
vv                                 AEBP1 MUTATED AEBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V8, binary
                 cls
clus                0   1
  AEBP1 MUTATED     0   4
  AEBP1 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      0    4
  AEBP1 WILD-TYPE   18  416
                        clus
vv                       AEBP1 MUTATED AEBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(92) Variable = SETD2 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED     6   2
  SETD2 WILD-TYPE 372  91
  SETD2 MUTATED SETD2 WILD-TYPE 
              8             463 
  SETD2 MUTATED SETD2 WILD-TYPE 
              2              91 
$`SETD2 MUTATED`
TCGA-DH-5140 TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-8164 TCGA-FG-6688 TCGA-FG-A6J3 
       19.96        30.21       211.17        21.40        18.77        22.26 
TCGA-HT-7684 TCGA-HT-A74H 
        6.05         2.43 

$`SETD2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       36.82        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y 
       14.76        17.82        16.41        15.02        16.44        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
        6.38        17.52        17.65        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  SETD2 MUTATED SETD2 WILD-TYPE 
           2.43            0.03 
  SETD2 MUTATED SETD2 WILD-TYPE 
         211.17          182.33 
  SETD2 MUTATED SETD2 WILD-TYPE 
          20.68           18.51 
[1] "2.4 - 211.2 (20.7)" "0.0 - 182.3 (18.5)"
[1] "hr=" "1.2"
D92V2, continuous
D92V3, binary
                 cls
clus                0   1
  SETD2 MUTATED     4   4
  SETD2 WILD-TYPE 203 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      4    4
  SETD2 WILD-TYPE  203  262
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             4             203
  MALE               4             262
[1] 2 2
[1] FALSE
D92V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SETD2 MUTATED             4                2                 2
  SETD2 WILD-TYPE         171              117               177
D92V5, multiclass
                   clus
vv                  SETD2 MUTATED SETD2 WILD-TYPE
  ASTROCYTOMA                   4             171
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V6, binary
                 cls
clus                0   1
  SETD2 MUTATED     3   5
  SETD2 WILD-TYPE  89 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      3    5
  SETD2 WILD-TYPE   89  376
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO              3              89
  YES             5             376
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           1     7
  SETD2 WILD-TYPE                        14   431
D92V7, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    1              14
  WHITE                                        7             431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V8, binary
                 cls
clus                0   1
  SETD2 MUTATED     0   8
  SETD2 WILD-TYPE  18 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0    8
  SETD2 WILD-TYPE   18  412
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             8             412
[1] 2 2
[1] FALSE

Clustering(93) Variable = DST MUTATION ANALYSIS
D93V1, survival
               sevent
clus2             0   1
  DST MUTATED    10   0
  DST WILD-TYPE 368  93
  DST MUTATED DST WILD-TYPE 
           10           461 
  DST MUTATED DST WILD-TYPE 
            0            93 
$`DST MUTATED`
TCGA-DB-A64S TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-6392 TCGA-FG-7637 TCGA-HT-7684 
       27.45        17.19        54.25       211.17        40.08         6.05 
TCGA-HT-7694 TCGA-HT-8010 TCGA-TQ-A7RH TCGA-VV-A829 
        6.90         1.64        15.98        37.05 

$`DST WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
        5.98        31.40        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       27.81        17.19        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
       44.68        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96        17.52        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.61        14.93        23.80        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M 
       13.51         0.10         7.89        35.93        23.47        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DST MUTATED DST WILD-TYPE 
         1.64          0.03 
  DST MUTATED DST WILD-TYPE 
       211.17        182.33 
  DST MUTATED DST WILD-TYPE 
        22.32         18.61 
[1] "1.6 - 211.2 (22.3)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D93V2, continuous
D93V3, binary
               cls
clus              0   1
  DST MUTATED     4   7
  DST WILD-TYPE 203 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED      4    7
  DST WILD-TYPE  203  259
        clus
vv       DST MUTATED DST WILD-TYPE
  FEMALE           4           203
  MALE             7           259
[1] 2 2
[1] FALSE
D93V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DST MUTATED             1                5                 5
  DST WILD-TYPE         174              114               174
D93V5, multiclass
                   clus
vv                  DST MUTATED DST WILD-TYPE
  ASTROCYTOMA                 1           174
  OLIGOASTROCYTOMA            5           114
  OLIGODENDROGLIOMA           5           174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V6, binary
               cls
clus              0   1
  DST MUTATED     2   9
  DST WILD-TYPE  90 372
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED      2    9
  DST WILD-TYPE   90  372
     clus
vv    DST MUTATED DST WILD-TYPE
  NO            2            90
  YES           9           372
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DST MUTATED                                  0     0
  DST WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DST MUTATED                           0    10
  DST WILD-TYPE                        15   428
D93V7, multiclass
                                  clus
vv                                 DST MUTATED DST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                     10           428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V8, binary
               cls
clus              0   1
  DST MUTATED     2   9
  DST WILD-TYPE  16 411
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED      2    9
  DST WILD-TYPE   16  411
                        clus
vv                       DST MUTATED DST WILD-TYPE
  HISPANIC OR LATINO               2            16
  NOT HISPANIC OR LATINO           9           411
[1] 2 2
[1] FALSE

Clustering(94) Variable = USP6 MUTATION ANALYSIS
D94V1, survival
                sevent
clus2              0   1
  USP6 MUTATED     4   1
  USP6 WILD-TYPE 374  92
  USP6 MUTATED USP6 WILD-TYPE 
             5            466 
  USP6 MUTATED USP6 WILD-TYPE 
             1             92 
$`USP6 MUTATED`
TCGA-DU-6392 TCGA-DU-A7TA TCGA-E1-5311 TCGA-FG-6688 TCGA-S9-A7R7 
      211.17        77.88       134.27        18.77        98.63 

$`USP6 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
       17.98       124.50        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       34.36        36.82        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       99.06        30.05        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  USP6 MUTATED USP6 WILD-TYPE 
         18.77           0.03 
  USP6 MUTATED USP6 WILD-TYPE 
        211.17         182.33 
  USP6 MUTATED USP6 WILD-TYPE 
        98.630         18.475 
[1] "18.8 - 211.2 (98.6)" "0.0 - 182.3 (18.5)" 
[1] "hr=" "5"  
D94V2, continuous
D94V3, binary
                cls
clus               0   1
  USP6 MUTATED     2   3
  USP6 WILD-TYPE 205 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP6 MUTATED      2    3
  USP6 WILD-TYPE  205  263
        clus
vv       USP6 MUTATED USP6 WILD-TYPE
  FEMALE            2            205
  MALE              3            263
[1] 2 2
[1] FALSE
D94V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  USP6 MUTATED             3                0                 2
  USP6 WILD-TYPE         172              119               177
D94V5, multiclass
                   clus
vv                  USP6 MUTATED USP6 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V6, binary
                cls
clus               0   1
  USP6 MUTATED     2   3
  USP6 WILD-TYPE  90 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP6 MUTATED      2    3
  USP6 WILD-TYPE   90  378
     clus
vv    USP6 MUTATED USP6 WILD-TYPE
  NO             2             90
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP6 MUTATED                                  0     0
  USP6 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USP6 MUTATED                           1     4
  USP6 WILD-TYPE                        14   434
D94V7, multiclass
                                  clus
vv                                 USP6 MUTATED USP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   1             14
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V8, binary
                cls
clus               0   1
  USP6 MUTATED     0   5
  USP6 WILD-TYPE  18 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP6 MUTATED      0    5
  USP6 WILD-TYPE   18  415
                        clus
vv                       USP6 MUTATED USP6 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            415
[1] 2 2
[1] FALSE

Clustering(95) Variable = TPM1 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  TPM1 MUTATED     5   0
  TPM1 WILD-TYPE 373  93
  TPM1 MUTATED TPM1 WILD-TYPE 
             5            466 
  TPM1 MUTATED TPM1 WILD-TYPE 
             0             93 
$`TPM1 MUTATED`
TCGA-DU-5849 TCGA-DU-6392 TCGA-FG-7643 TCGA-IK-8125 TCGA-S9-A7QZ 
       14.56       211.17        20.09        42.77        13.02 

$`TPM1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       13.38         3.45        18.61        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        19.00        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        28.37       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  TPM1 MUTATED TPM1 WILD-TYPE 
         13.02           0.03 
  TPM1 MUTATED TPM1 WILD-TYPE 
        211.17         182.33 
  TPM1 MUTATED TPM1 WILD-TYPE 
         20.09          18.61 
[1] "13.0 - 211.2 (20.1)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D95V2, continuous
D95V3, binary
                cls
clus               0   1
  TPM1 MUTATED     2   3
  TPM1 WILD-TYPE 205 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM1 MUTATED      2    3
  TPM1 WILD-TYPE  205  263
        clus
vv       TPM1 MUTATED TPM1 WILD-TYPE
  FEMALE            2            205
  MALE              3            263
[1] 2 2
[1] FALSE
D95V4, continuous
[1] "Remove cluster labels:" "TPM1 MUTATED"          
clus
  TPM1 MUTATED TPM1 WILD-TYPE 
             1            268 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-8168     TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-A5TU     TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-A6S7     TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-A7T8     TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-DU-A7TD     TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-E1-5304     TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-E1-A7YV     TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-5965     TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-6691     TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-8185     TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-8189     TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-A60J     TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-FG-A711     TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-7470     TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-7607     TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-7692     TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-7875     TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-A5R7     TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-A617     TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-HT-A61C     TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-KT-A7W1     TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-P5-A5EX     TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-P5-A5F6     TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-QH-A65V     TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-QH-A6CU     TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-QH-A6CY     TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-QH-A6X5     TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-QH-A6XC     TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-RY-A840     TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6TU     TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6TY     TCGA-S9-A6TZ     TCGA-S9-A6U0     TCGA-S9-A6U1 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6U2     TCGA-S9-A6U5     TCGA-S9-A6U6     TCGA-S9-A6U8 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6UA     TCGA-S9-A6UB     TCGA-S9-A6WD     TCGA-S9-A6WE 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6WG     TCGA-S9-A6WH     TCGA-S9-A6WI     TCGA-S9-A6WL 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6WM     TCGA-S9-A6WN     TCGA-S9-A6WO     TCGA-S9-A6WP 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A6WQ     TCGA-S9-A7IQ     TCGA-S9-A7IS     TCGA-S9-A7IX 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A7IY     TCGA-S9-A7IZ     TCGA-S9-A7J0     TCGA-S9-A7J1 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A7J2     TCGA-S9-A7J3     TCGA-S9-A7QW     TCGA-S9-A7QX 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A7QY     TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A7R4     TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-S9-A89Z     TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-TM-A7CA     TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-TM-A84F     TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-TM-A84J     TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-TM-A84Q     TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-TQ-A7RW     TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
    TCGA-VM-A8CE     TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" "TPM1 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TPM1 MUTATED             1                2                 2
  TPM1 WILD-TYPE         174              117               177
D95V5, multiclass
                   clus
vv                  TPM1 MUTATED TPM1 WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V6, binary
                cls
clus               0   1
  TPM1 MUTATED     1   4
  TPM1 WILD-TYPE  91 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM1 MUTATED      1    4
  TPM1 WILD-TYPE   91  377
     clus
vv    TPM1 MUTATED TPM1 WILD-TYPE
  NO             1             91
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPM1 MUTATED                                  0     0
  TPM1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPM1 MUTATED                           0     5
  TPM1 WILD-TYPE                        15   433
D95V7, multiclass
                                  clus
vv                                 TPM1 MUTATED TPM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V8, binary
                cls
clus               0   1
  TPM1 MUTATED     0   5
  TPM1 WILD-TYPE  18 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM1 MUTATED      0    5
  TPM1 WILD-TYPE   18  415
                        clus
vv                       TPM1 MUTATED TPM1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            415
[1] 2 2
[1] FALSE

Clustering(96) Variable = GLYAT MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2               0   1
  GLYAT MUTATED     4   0
  GLYAT WILD-TYPE 374  93
  GLYAT MUTATED GLYAT WILD-TYPE 
              4             467 
  GLYAT MUTATED GLYAT WILD-TYPE 
              0              93 
$`GLYAT MUTATED`
TCGA-CS-4943 TCGA-DU-6392 TCGA-S9-A6UB TCGA-WY-A85D 
       18.15       211.17       106.39        37.71 

$`GLYAT WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93         5.85        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        20.81 

  GLYAT MUTATED GLYAT WILD-TYPE 
          18.15            0.03 
  GLYAT MUTATED GLYAT WILD-TYPE 
         211.17          182.33 
  GLYAT MUTATED GLYAT WILD-TYPE 
          72.05           18.61 
[1] "18.1 - 211.2 (72.0)" "0.0 - 182.3 (18.6)" 
[1] "hr="     "2.7e+07"
D96V2, continuous
D96V3, binary
                 cls
clus                0   1
  GLYAT MUTATED     1   3
  GLYAT WILD-TYPE 206 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYAT MUTATED      1    3
  GLYAT WILD-TYPE  206  263
        clus
vv       GLYAT MUTATED GLYAT WILD-TYPE
  FEMALE             1             206
  MALE               3             263
[1] 2 2
[1] FALSE
D96V4, continuous
[1] "Remove cluster labels:" "GLYAT MUTATED"         
clus
  GLYAT MUTATED GLYAT WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4944 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395      TCGA-CS-5396 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6290 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667      TCGA-CS-6668 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE      TCGA-DB-A64L 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S      TCGA-DB-A64U 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X      TCGA-DB-A75L 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D      TCGA-DH-A66F 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU      TCGA-DH-A7UV 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5874 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"GLYAT WILD-TYPE" "GLYAT WILD-TYPE" "GLYAT WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  GLYAT MUTATED             2                1                 1
  GLYAT WILD-TYPE         173              118               178
D96V5, multiclass
                   clus
vv                  GLYAT MUTATED GLYAT WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V6, binary
                 cls
clus                0   1
  GLYAT MUTATED     1   3
  GLYAT WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYAT MUTATED      1    3
  GLYAT WILD-TYPE   91  378
     clus
vv    GLYAT MUTATED GLYAT WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLYAT MUTATED                                  0     0
  GLYAT WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLYAT MUTATED                           0     4
  GLYAT WILD-TYPE                        15   434
D96V7, multiclass
                                  clus
vv                                 GLYAT MUTATED GLYAT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V8, binary
                 cls
clus                0   1
  GLYAT MUTATED     0   2
  GLYAT WILD-TYPE  18 418
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYAT MUTATED      0    2
  GLYAT WILD-TYPE   18  418
                        clus
vv                       GLYAT MUTATED GLYAT WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             2             418
[1] 2 2
[1] FALSE

Clustering(97) Variable = DIAPH1 MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  DIAPH1 MUTATED     4   0
  DIAPH1 WILD-TYPE 374  93
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               4              467 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               0               93 
$`DIAPH1 MUTATED`
TCGA-DU-6392 TCGA-FG-7643 TCGA-FG-8185 TCGA-TM-A84Q 
      211.17        20.09        14.24        25.38 

$`DIAPH1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       22.55        20.61        12.95        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
           14.24             0.03 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
          211.17           182.33 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
          22.735           18.610 
[1] "14.2 - 211.2 (22.7)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D97V2, continuous
D97V3, binary
                  cls
clus                 0   1
  DIAPH1 MUTATED     2   2
  DIAPH1 WILD-TYPE 205 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH1 MUTATED      2    2
  DIAPH1 WILD-TYPE  205  264
        clus
vv       DIAPH1 MUTATED DIAPH1 WILD-TYPE
  FEMALE              2              205
  MALE                2              264
[1] 2 2
[1] FALSE
D97V4, continuous
[1] "Remove cluster labels:" "DIAPH1 MUTATED"        
clus
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               2              267 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T       TCGA-TQ-A7RW 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD       TCGA-VM-A8CE 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DIAPH1 MUTATED             3                1                 0
  DIAPH1 WILD-TYPE         172              118               179
D97V5, multiclass
                   clus
vv                  DIAPH1 MUTATED DIAPH1 WILD-TYPE
  ASTROCYTOMA                    3              172
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              0              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V6, binary
                  cls
clus                 0   1
  DIAPH1 MUTATED     1   3
  DIAPH1 WILD-TYPE  91 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH1 MUTATED      1    3
  DIAPH1 WILD-TYPE   91  378
     clus
vv    DIAPH1 MUTATED DIAPH1 WILD-TYPE
  NO               1               91
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIAPH1 MUTATED                                  0     0
  DIAPH1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIAPH1 MUTATED                           0     4
  DIAPH1 WILD-TYPE                        15   434
D97V7, multiclass
                                  clus
vv                                 DIAPH1 MUTATED DIAPH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V8, binary
                  cls
clus                 0   1
  DIAPH1 MUTATED     0   4
  DIAPH1 WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH1 MUTATED      0    4
  DIAPH1 WILD-TYPE   18  416
                        clus
vv                       DIAPH1 MUTATED DIAPH1 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(98) Variable = ZMYM2 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2               0   1
  ZMYM2 MUTATED     5   1
  ZMYM2 WILD-TYPE 373  92
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              6             465 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              92 
$`ZMYM2 MUTATED`
TCGA-DU-6392 TCGA-DU-7013 TCGA-DU-A6S6 TCGA-FG-5962 TCGA-FG-A4MX TCGA-HT-7875 
      211.17         8.84        77.98        47.77        18.71         0.33 

$`ZMYM2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65        12.20         8.65         2.70         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MY 
       22.52        32.61        38.27        10.72        18.38        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       23.61        37.15         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
           0.33            0.03 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
         211.17          182.33 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          33.24           18.61 
[1] "0.3 - 211.2 (33.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.8"
D98V2, continuous
D98V3, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     2   4
  ZMYM2 WILD-TYPE 205 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      2    4
  ZMYM2 WILD-TYPE  205  262
        clus
vv       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  FEMALE             2             205
  MALE               4             262
[1] 2 2
[1] FALSE
D98V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZMYM2 MUTATED             3                1                 2
  ZMYM2 WILD-TYPE         172              118               177
D98V5, multiclass
                   clus
vv                  ZMYM2 MUTATED ZMYM2 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V6, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     2   4
  ZMYM2 WILD-TYPE  90 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      2    4
  ZMYM2 WILD-TYPE   90  377
     clus
vv    ZMYM2 MUTATED ZMYM2 WILD-TYPE
  NO              2              90
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYM2 MUTATED                                  0     0
  ZMYM2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMYM2 MUTATED                           0     6
  ZMYM2 WILD-TYPE                        15   432
D98V7, multiclass
                                  clus
vv                                 ZMYM2 MUTATED ZMYM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V8, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0   6
  ZMYM2 WILD-TYPE  18 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0    6
  ZMYM2 WILD-TYPE   18  414
                        clus
vv                       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             414
[1] 2 2
[1] FALSE

Clustering(99) Variable = HCFC1 MUTATION ANALYSIS
D99V1, survival
                 sevent
clus2               0   1
  HCFC1 MUTATED     6   1
  HCFC1 WILD-TYPE 372  92
  HCFC1 MUTATED HCFC1 WILD-TYPE 
              7             464 
  HCFC1 MUTATED HCFC1 WILD-TYPE 
              1              92 
$`HCFC1 MUTATED`
TCGA-DU-6392 TCGA-DU-A5TU TCGA-HT-7607 TCGA-KT-A7W1 TCGA-QH-A6CU TCGA-S9-A7QX 
      211.17         3.65         3.16        14.40        14.83        13.12 
TCGA-S9-A7R3 
       99.06 

$`HCFC1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 
       29.85        23.18       122.47         4.57        17.29        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02       169.84        10.39        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  HCFC1 MUTATED HCFC1 WILD-TYPE 
           3.16            0.03 
  HCFC1 MUTATED HCFC1 WILD-TYPE 
         211.17          182.33 
  HCFC1 MUTATED HCFC1 WILD-TYPE 
          14.40           18.66 
[1] "3.2 - 211.2 (14.4)" "0.0 - 182.3 (18.7)"
[1] "hr=" "2.8"
D99V2, continuous
D99V3, binary
                 cls
clus                0   1
  HCFC1 MUTATED     7   0
  HCFC1 WILD-TYPE 200 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCFC1 MUTATED      7    0
  HCFC1 WILD-TYPE  200  266
        clus
vv       HCFC1 MUTATED HCFC1 WILD-TYPE
  FEMALE             7             200
  MALE               0             266
[1] 2 2
[1] FALSE
D99V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HCFC1 MUTATED             6                0                 1
  HCFC1 WILD-TYPE         169              119               178
D99V5, multiclass
                   clus
vv                  HCFC1 MUTATED HCFC1 WILD-TYPE
  ASTROCYTOMA                   6             169
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V6, binary
                 cls
clus                0   1
  HCFC1 MUTATED     1   6
  HCFC1 WILD-TYPE  91 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCFC1 MUTATED      1    6
  HCFC1 WILD-TYPE   91  375
     clus
vv    HCFC1 MUTATED HCFC1 WILD-TYPE
  NO              1              91
  YES             6             375
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCFC1 MUTATED                                  0     0
  HCFC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HCFC1 MUTATED                           0     7
  HCFC1 WILD-TYPE                        15   431
D99V7, multiclass
                                  clus
vv                                 HCFC1 MUTATED HCFC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        7             431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V8, binary
                 cls
clus                0   1
  HCFC1 MUTATED     0   7
  HCFC1 WILD-TYPE  18 413
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCFC1 MUTATED      0    7
  HCFC1 WILD-TYPE   18  413
                        clus
vv                       HCFC1 MUTATED HCFC1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             7             413
[1] 2 2
[1] FALSE

Clustering(100) Variable = MST1 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2              0   1
  MST1 MUTATED     4   0
  MST1 WILD-TYPE 374  93
  MST1 MUTATED MST1 WILD-TYPE 
             4            467 
  MST1 MUTATED MST1 WILD-TYPE 
             0             93 
$`MST1 MUTATED`
TCGA-DB-A64R TCGA-DU-6392 TCGA-FG-A4MT TCGA-HT-A5RA 
       31.40       211.17        38.27        27.35 

$`MST1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
        5.98        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        32.61        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  MST1 MUTATED MST1 WILD-TYPE 
         27.35           0.03 
  MST1 MUTATED MST1 WILD-TYPE 
        211.17         182.33 
  MST1 MUTATED MST1 WILD-TYPE 
        34.835         18.510 
[1] "27.4 - 211.2 (34.8)" "0.0 - 182.3 (18.5)" 
[1] "hr="   "1e+07"
D100V2, continuous
D100V3, binary
                cls
clus               0   1
  MST1 MUTATED     4   0
  MST1 WILD-TYPE 203 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      4    0
  MST1 WILD-TYPE  203  266
        clus
vv       MST1 MUTATED MST1 WILD-TYPE
  FEMALE            4            203
  MALE              0            266
[1] 2 2
[1] FALSE
D100V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MST1 MUTATED             2                0                 2
  MST1 WILD-TYPE         173              119               177
D100V5, multiclass
                   clus
vv                  MST1 MUTATED MST1 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V6, binary
                cls
clus               0   1
  MST1 MUTATED     1   3
  MST1 WILD-TYPE  91 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      1    3
  MST1 WILD-TYPE   91  378
     clus
vv    MST1 MUTATED MST1 WILD-TYPE
  NO             1             91
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST1 MUTATED                                  0     0
  MST1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MST1 MUTATED                           0     3
  MST1 WILD-TYPE                        15   435
D100V7, multiclass
                                  clus
vv                                 MST1 MUTATED MST1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V8, binary
                cls
clus               0   1
  MST1 MUTATED     1   3
  MST1 WILD-TYPE  17 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      1    3
  MST1 WILD-TYPE   17  417
                        clus
vv                       MST1 MUTATED MST1 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(101) Variable = TNFSF14 MUTATION ANALYSIS
D101V1, survival
                   sevent
clus2                 0   1
  TNFSF14 MUTATED     2   3
  TNFSF14 WILD-TYPE 376  90
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
                5               466 
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
                3                90 
$`TNFSF14 MUTATED`
TCGA-DU-A7T6 TCGA-DU-A7TD TCGA-HT-7687 TCGA-TM-A7C3 TCGA-TM-A84B 
       17.98         7.50         0.10        49.45        24.92 

$`TNFSF14 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       21.30       124.50        77.88        42.31        23.51        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       11.97        48.33        49.32        34.78        48.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
             0.10              0.03 
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
            49.45            211.17 
  TNFSF14 MUTATED TNFSF14 WILD-TYPE 
            17.98             18.61 
[1] "0.1 - 49.5 (18.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "4.8"
D101V2, continuous
D101V3, binary
                   cls
clus                  0   1
  TNFSF14 MUTATED     2   3
  TNFSF14 WILD-TYPE 205 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF14 MUTATED      2    3
  TNFSF14 WILD-TYPE  205  263
        clus
vv       TNFSF14 MUTATED TNFSF14 WILD-TYPE
  FEMALE               2               205
  MALE                 3               263
[1] 2 2
[1] FALSE
D101V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TNFSF14 MUTATED             2                1                 2
  TNFSF14 WILD-TYPE         173              118               177
D101V5, multiclass
                   clus
vv                  TNFSF14 MUTATED TNFSF14 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               2               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V6, binary
                   cls
clus                  0   1
  TNFSF14 MUTATED     0   5
  TNFSF14 WILD-TYPE  92 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF14 MUTATED      0    5
  TNFSF14 WILD-TYPE   92  376
     clus
vv    TNFSF14 MUTATED TNFSF14 WILD-TYPE
  NO                0                92
  YES               5               376
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFSF14 MUTATED                                  0     0
  TNFSF14 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TNFSF14 MUTATED                           0     5
  TNFSF14 WILD-TYPE                        15   433
D101V7, multiclass
                                  clus
vv                                 TNFSF14 MUTATED TNFSF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          5               433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V8, binary
                   cls
clus                  0   1
  TNFSF14 MUTATED     0   5
  TNFSF14 WILD-TYPE  18 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF14 MUTATED      0    5
  TNFSF14 WILD-TYPE   18  415
                        clus
vv                       TNFSF14 MUTATED TNFSF14 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               5               415
[1] 2 2
[1] FALSE

Clustering(102) Variable = DNAH7 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2               0   1
  DNAH7 MUTATED     7   3
  DNAH7 WILD-TYPE 371  90
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             10             461 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              3              90 
$`DNAH7 MUTATED`
TCGA-DB-A75K TCGA-DB-A75M TCGA-DU-6392 TCGA-DU-7019 TCGA-DU-8158 TCGA-DU-A76R 
       12.10        17.88       211.17        26.30         5.10        21.30 
TCGA-FG-6692 TCGA-HT-7477 TCGA-P5-A733 TCGA-S9-A7IY 
       18.44        24.26        13.61        23.51 

$`DNAH7 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       18.51        11.24        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
        7.13        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       14.93        24.99        23.97        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R 
       10.42        13.25        11.64         0.20         9.01        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DNAH7 MUTATED DNAH7 WILD-TYPE 
           5.10            0.03 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
         211.17          182.33 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          19.87           18.61 
[1] "5.1 - 211.2 (19.9)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.2"
D102V2, continuous
D102V3, binary
                 cls
clus                0   1
  DNAH7 MUTATED     4   6
  DNAH7 WILD-TYPE 203 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      4    6
  DNAH7 WILD-TYPE  203  260
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE             4             203
  MALE               6             260
[1] 2 2
[1] FALSE
D102V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DNAH7 MUTATED             5                3                 2
  DNAH7 WILD-TYPE         170              116               177
D102V5, multiclass
                   clus
vv                  DNAH7 MUTATED DNAH7 WILD-TYPE
  ASTROCYTOMA                   5             170
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V6, binary
                 cls
clus                0   1
  DNAH7 MUTATED     3   7
  DNAH7 WILD-TYPE  89 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      3    7
  DNAH7 WILD-TYPE   89  374
     clus
vv    DNAH7 MUTATED DNAH7 WILD-TYPE
  NO              3              89
  YES             7             374
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH7 MUTATED                                  0     0
  DNAH7 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH7 MUTATED                           0    10
  DNAH7 WILD-TYPE                        15   428
D102V7, multiclass
                                  clus
vv                                 DNAH7 MUTATED DNAH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                       10             428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V8, binary
                 cls
clus                0   1
  DNAH7 MUTATED     0  10
  DNAH7 WILD-TYPE  18 410
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0   10
  DNAH7 WILD-TYPE   18  410
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            10             410
[1] 2 2
[1] FALSE

Clustering(103) Variable = ENGASE MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  ENGASE MUTATED     2   1
  ENGASE WILD-TYPE 376  92
  ENGASE MUTATED ENGASE WILD-TYPE 
               3              468 
  ENGASE MUTATED ENGASE WILD-TYPE 
               1               92 
$`ENGASE MUTATED`
TCGA-DU-6392 TCGA-E1-5305 TCGA-S9-A6U2 
      211.17        79.99        23.64 

$`ENGASE WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
       44.42         0.56        50.14        67.46        41.13        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 
       34.49        31.33        28.70        22.95        17.62        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  ENGASE MUTATED ENGASE WILD-TYPE 
           23.64             0.03 
  ENGASE MUTATED ENGASE WILD-TYPE 
          211.17           182.33 
  ENGASE MUTATED ENGASE WILD-TYPE 
           79.99            18.56 
[1] "23.6 - 211.2 (80.0)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.5"
D103V2, continuous
D103V3, binary
                  cls
clus                 0   1
  ENGASE MUTATED     2   1
  ENGASE WILD-TYPE 205 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      2    1
  ENGASE WILD-TYPE  205  265
        clus
vv       ENGASE MUTATED ENGASE WILD-TYPE
  FEMALE              2              205
  MALE                1              265
[1] 2 2
[1] FALSE
D103V4, continuous
[1] "Remove cluster labels:" "ENGASE MUTATED"        
clus
  ENGASE MUTATED ENGASE WILD-TYPE 
               2              267 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO       TCGA-E1-A7YV 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963       TCGA-FG-5965 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U5 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA       TCGA-S9-A6UB 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG       TCGA-S9-A6WH 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM       TCGA-S9-A6WN 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ       TCGA-S9-A7IQ 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY       TCGA-S9-A7IZ 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2       TCGA-S9-A7J3 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY       TCGA-S9-A7QZ 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3       TCGA-S9-A7R4 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V       TCGA-S9-A89Z 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5       TCGA-TM-A7CA 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C       TCGA-TM-A84F 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I       TCGA-TM-A84J 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O       TCGA-TM-A84Q 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T       TCGA-TQ-A7RW 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD       TCGA-VM-A8CE 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
      TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"ENGASE WILD-TYPE" "ENGASE WILD-TYPE" "ENGASE WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ENGASE MUTATED             2                0                 1
  ENGASE WILD-TYPE         173              119               178
D103V5, multiclass
                   clus
vv                  ENGASE MUTATED ENGASE WILD-TYPE
  ASTROCYTOMA                    2              173
  OLIGOASTROCYTOMA               0              119
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V6, binary
                  cls
clus                 0   1
  ENGASE MUTATED     1   2
  ENGASE WILD-TYPE  91 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      1    2
  ENGASE WILD-TYPE   91  379
     clus
vv    ENGASE MUTATED ENGASE WILD-TYPE
  NO               1               91
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENGASE MUTATED                                  0     0
  ENGASE WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ENGASE MUTATED                           0     3
  ENGASE WILD-TYPE                        15   435
D103V7, multiclass
                                  clus
vv                                 ENGASE MUTATED ENGASE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V8, binary
                  cls
clus                 0   1
  ENGASE MUTATED     0   3
  ENGASE WILD-TYPE  18 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      0    3
  ENGASE WILD-TYPE   18  417
                        clus
vv                       ENGASE MUTATED ENGASE WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              3              417
[1] 2 2
[1] FALSE

Clustering(104) Variable = MYH8 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2              0   1
  MYH8 MUTATED    11   0
  MYH8 WILD-TYPE 367  93
  MYH8 MUTATED MYH8 WILD-TYPE 
            11            460 
  MYH8 MUTATED MYH8 WILD-TYPE 
             0             93 
$`MYH8 MUTATED`
TCGA-DH-5142 TCGA-DU-6392 TCGA-DU-A5TW TCGA-FG-A6J3 TCGA-HT-7480 TCGA-HT-7608 
       30.31       211.17         5.65        22.26        75.19        22.06 
TCGA-HT-7860 TCGA-HT-8564 TCGA-P5-A731 TCGA-QH-A65R TCGA-TM-A7C4 
        0.49        15.72         9.01        15.16        48.33 

$`MYH8 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 
        6.54        24.26         6.38        40.34        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29         3.16        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        13.74        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A733 TCGA-QH-A65S 
       10.42        13.25        11.64         0.20        13.61         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  MYH8 MUTATED MYH8 WILD-TYPE 
          0.49           0.03 
  MYH8 MUTATED MYH8 WILD-TYPE 
        211.17         182.33 
  MYH8 MUTATED MYH8 WILD-TYPE 
         22.06          18.61 
[1] "0.5 - 211.2 (22.1)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D104V2, continuous
D104V3, binary
                cls
clus               0   1
  MYH8 MUTATED     7   4
  MYH8 WILD-TYPE 200 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH8 MUTATED      7    4
  MYH8 WILD-TYPE  200  262
        clus
vv       MYH8 MUTATED MYH8 WILD-TYPE
  FEMALE            7            200
  MALE              4            262
[1] 2 2
[1] FALSE
D104V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MYH8 MUTATED             7                2                 2
  MYH8 WILD-TYPE         168              117               177
D104V5, multiclass
                   clus
vv                  MYH8 MUTATED MYH8 WILD-TYPE
  ASTROCYTOMA                  7            168
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V6, binary
                cls
clus               0   1
  MYH8 MUTATED     3   8
  MYH8 WILD-TYPE  89 373
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH8 MUTATED      3    8
  MYH8 WILD-TYPE   89  373
     clus
vv    MYH8 MUTATED MYH8 WILD-TYPE
  NO             3             89
  YES            8            373
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH8 MUTATED                                  0     0
  MYH8 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH8 MUTATED                           2     9
  MYH8 WILD-TYPE                        13   429
D104V7, multiclass
                                  clus
vv                                 MYH8 MUTATED MYH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   2             13
  WHITE                                       9            429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V8, binary
                cls
clus               0   1
  MYH8 MUTATED     1  10
  MYH8 WILD-TYPE  17 410
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH8 MUTATED      1   10
  MYH8 WILD-TYPE   17  410
                        clus
vv                       MYH8 MUTATED MYH8 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO           10            410
[1] 2 2
[1] FALSE

Clustering(105) Variable = VSIG4 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  VSIG4 MUTATED     5   1
  VSIG4 WILD-TYPE 373  92
  VSIG4 MUTATED VSIG4 WILD-TYPE 
              6             465 
  VSIG4 MUTATED VSIG4 WILD-TYPE 
              1              92 
$`VSIG4 MUTATED`
TCGA-CS-6668 TCGA-DB-A4XF TCGA-DB-A75K TCGA-FG-8182 TCGA-HT-8018 TCGA-P5-A72X 
        8.02        33.57        12.10        13.68        37.87        13.25 

$`VSIG4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG 
       18.84        30.21        46.72        39.78        37.45        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        18.51        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55         0.10        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28         0.16        10.42        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  VSIG4 MUTATED VSIG4 WILD-TYPE 
           8.02            0.03 
  VSIG4 MUTATED VSIG4 WILD-TYPE 
          37.87          211.17 
  VSIG4 MUTATED VSIG4 WILD-TYPE 
         13.465          18.610 
[1] "8.0 - 37.9 (13.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.4"
D105V2, continuous
D105V3, binary
                 cls
clus                0   1
  VSIG4 MUTATED     4   2
  VSIG4 WILD-TYPE 203 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VSIG4 MUTATED      4    2
  VSIG4 WILD-TYPE  203  264
        clus
vv       VSIG4 MUTATED VSIG4 WILD-TYPE
  FEMALE             4             203
  MALE               2             264
[1] 2 2
[1] FALSE
D105V4, continuous
[1] "Remove cluster labels:" "VSIG4 MUTATED"         
clus
  VSIG4 MUTATED VSIG4 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE      TCGA-DB-A64L 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S      TCGA-DB-A64U 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X      TCGA-DB-A75L 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D      TCGA-DH-A66F 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU      TCGA-DH-A7UV 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5874 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" "VSIG4 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  VSIG4 MUTATED             2                2                 2
  VSIG4 WILD-TYPE         173              117               177
D105V5, multiclass
                   clus
vv                  VSIG4 MUTATED VSIG4 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V6, binary
                 cls
clus                0   1
  VSIG4 MUTATED     0   6
  VSIG4 WILD-TYPE  92 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VSIG4 MUTATED      0    6
  VSIG4 WILD-TYPE   92  375
     clus
vv    VSIG4 MUTATED VSIG4 WILD-TYPE
  NO              0              92
  YES             6             375
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VSIG4 MUTATED                                  0     0
  VSIG4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VSIG4 MUTATED                           0     6
  VSIG4 WILD-TYPE                        15   432
D105V7, multiclass
                                  clus
vv                                 VSIG4 MUTATED VSIG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        6             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V8, binary
                 cls
clus                0   1
  VSIG4 MUTATED     0   6
  VSIG4 WILD-TYPE  18 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VSIG4 MUTATED      0    6
  VSIG4 WILD-TYPE   18  414
                        clus
vv                       VSIG4 MUTATED VSIG4 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             414
[1] 2 2
[1] FALSE

Clustering(106) Variable = KRT3 MUTATION ANALYSIS
D106V1, survival
                sevent
clus2              0   1
  KRT3 MUTATED     2   2
  KRT3 WILD-TYPE 376  91
  KRT3 MUTATED KRT3 WILD-TYPE 
             4            467 
  KRT3 MUTATED KRT3 WILD-TYPE 
             2             91 
$`KRT3 MUTATED`
TCGA-DU-5854 TCGA-DU-6397 TCGA-IK-7675 TCGA-S9-A6WO 
        8.45        46.06        19.00        18.61 

$`KRT3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       15.91        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  KRT3 MUTATED KRT3 WILD-TYPE 
          8.45           0.03 
  KRT3 MUTATED KRT3 WILD-TYPE 
         46.06         211.17 
  KRT3 MUTATED KRT3 WILD-TYPE 
        18.805         18.610 
[1] "8.4 - 46.1 (18.8)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "3.4"
D106V2, continuous
D106V3, binary
                cls
clus               0   1
  KRT3 MUTATED     1   3
  KRT3 WILD-TYPE 206 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      1    3
  KRT3 WILD-TYPE  206  263
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  FEMALE            1            206
  MALE              3            263
[1] 2 2
[1] FALSE
D106V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  KRT3 MUTATED             2                0                 2
  KRT3 WILD-TYPE         173              119               177
D106V5, multiclass
                   clus
vv                  KRT3 MUTATED KRT3 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V6, binary
                cls
clus               0   1
  KRT3 MUTATED     2   2
  KRT3 WILD-TYPE  90 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      2    2
  KRT3 WILD-TYPE   90  379
     clus
vv    KRT3 MUTATED KRT3 WILD-TYPE
  NO             2             90
  YES            2            379
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT3 MUTATED                                  0     0
  KRT3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT3 MUTATED                           0     4
  KRT3 WILD-TYPE                        15   434
D106V7, multiclass
                                  clus
vv                                 KRT3 MUTATED KRT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V8, binary
                cls
clus               0   1
  KRT3 MUTATED     1   3
  KRT3 WILD-TYPE  17 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      1    3
  KRT3 WILD-TYPE   17  417
                        clus
vv                       KRT3 MUTATED KRT3 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(107) Variable = STAG2 MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     4   0
  STAG2 WILD-TYPE 374  93
  STAG2 MUTATED STAG2 WILD-TYPE 
              4             467 
  STAG2 MUTATED STAG2 WILD-TYPE 
              0              93 
$`STAG2 MUTATED`
TCGA-DU-6392 TCGA-HT-7610 TCGA-HT-8011 TCGA-TM-A7C3 
      211.17        56.09        16.24        49.45 

$`STAG2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43         1.64         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  STAG2 MUTATED STAG2 WILD-TYPE 
          16.24            0.03 
  STAG2 MUTATED STAG2 WILD-TYPE 
         211.17          182.33 
  STAG2 MUTATED STAG2 WILD-TYPE 
          52.77           18.61 
[1] "16.2 - 211.2 (52.8)" "0.0 - 182.3 (18.6)" 
[1] "hr="     "2.7e+07"
D107V2, continuous
D107V3, binary
                 cls
clus                0   1
  STAG2 MUTATED     3   1
  STAG2 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      3    1
  STAG2 WILD-TYPE  204  265
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D107V4, continuous
[1] "Remove cluster labels:" "STAG2 MUTATED"         
clus
  STAG2 MUTATED STAG2 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-HT-A61C      TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KT-A7W1      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-P5-A5F6      TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-QH-A65V      TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-QH-A6CU      TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-QH-A6CY      TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-QH-A6X5      TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-QH-A6XC      TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-RY-A840      TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6TU      TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6TY      TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6U2      TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6UA      TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6WG      TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6WM      TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A6WQ      TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A7IY      TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A7J2      TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A7QY      TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A7R3      TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-S9-A89V      TCGA-S9-A89Z      TCGA-TM-A7C4      TCGA-TM-A7C5 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  STAG2 MUTATED             3                1                 0
  STAG2 WILD-TYPE         172              118               179
D107V5, multiclass
                   clus
vv                  STAG2 MUTATED STAG2 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V6, binary
                 cls
clus                0   1
  STAG2 MUTATED     1   3
  STAG2 WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      1    3
  STAG2 WILD-TYPE   91  378
     clus
vv    STAG2 MUTATED STAG2 WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAG2 MUTATED                                  0     0
  STAG2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED                           0     4
  STAG2 WILD-TYPE                        15   434
D107V7, multiclass
                                  clus
vv                                 STAG2 MUTATED STAG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V8, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   4
  STAG2 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    4
  STAG2 WILD-TYPE   18  416
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(108) Variable = MUC17 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED    18   5
  MUC17 WILD-TYPE 360  88
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             448 
  MUC17 MUTATED MUC17 WILD-TYPE 
              5              88 
$`MUC17 MUTATED`
TCGA-DB-A64L TCGA-DH-A7UR TCGA-DU-6392 TCGA-DU-6396 TCGA-DU-7007 TCGA-DU-7012 
       24.20        54.25       211.17        75.16        62.96         6.54 
TCGA-DU-8166 TCGA-DU-A5TW TCGA-HT-7605 TCGA-HT-7687 TCGA-HT-7854 TCGA-HT-7875 
       16.96         5.65         4.57         0.10        39.48         0.33 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-A5R7 TCGA-HT-A74H TCGA-QH-A870 TCGA-S9-A6TS 
       31.43         0.10        20.22         2.43        12.99        62.17 
TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A7R8 TCGA-TM-A84J TCGA-WY-A859 
       69.50        31.10        31.59        24.16        39.88 

$`MUC17 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        17.19        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99       105.21         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18       122.47        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
       16.24         0.76        44.68         6.05        42.74        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       23.61        37.15         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        3.72        11.28         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
       17.65        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        9.90        28.08         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
        5.85       106.39        72.59        80.12        32.45        84.99 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
      169.84        10.39        99.06        30.05        98.63        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A 
       23.21         8.05        51.06        13.32        43.96        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  MUC17 MUTATED MUC17 WILD-TYPE 
           0.10            0.03 
  MUC17 MUTATED MUC17 WILD-TYPE 
         211.17          182.33 
  MUC17 MUTATED MUC17 WILD-TYPE 
         24.200          18.475 
[1] "0.1 - 211.2 (24.2)" "0.0 - 182.3 (18.5)"
[1] "hr=" "1.2"
D108V2, continuous
D108V3, binary
                 cls
clus                0   1
  MUC17 MUTATED    13  11
  MUC17 WILD-TYPE 194 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     13   11
  MUC17 WILD-TYPE  194  255
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE            13             194
  MALE              11             255
[1] 2 2
[1] FALSE
D108V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MUC17 MUTATED            13                4                 7
  MUC17 WILD-TYPE         162              115               172
D108V5, multiclass
                   clus
vv                  MUC17 MUTATED MUC17 WILD-TYPE
  ASTROCYTOMA                  13             162
  OLIGOASTROCYTOMA              4             115
  OLIGODENDROGLIOMA             7             172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V6, binary
                 cls
clus                0   1
  MUC17 MUTATED     4  20
  MUC17 WILD-TYPE  88 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      4   20
  MUC17 WILD-TYPE   88  361
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO              4              88
  YES            20             361
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC17 MUTATED                                  0     0
  MUC17 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED                           2    22
  MUC17 WILD-TYPE                        13   416
D108V7, multiclass
                                  clus
vv                                 MUC17 MUTATED MUC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    2              13
  WHITE                                       22             416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V8, binary
                 cls
clus                0   1
  MUC17 MUTATED     0  23
  MUC17 WILD-TYPE  18 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      0   23
  MUC17 WILD-TYPE   18  397
                        clus
vv                       MUC17 MUTATED MUC17 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            23             397
[1] 2 2
[1] FALSE

Clustering(109) Variable = ABCA7 MUTATION ANALYSIS
D109V1, survival
                 sevent
clus2               0   1
  ABCA7 MUTATED     6   3
  ABCA7 WILD-TYPE 372  90
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              9             462 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              3              90 
$`ABCA7 MUTATED`
TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-7010 TCGA-DU-A7TC TCGA-FG-A4MW TCGA-HT-7854 
       30.21       211.17        14.99        23.51        18.38        39.48 
TCGA-P5-A5EW TCGA-TM-A84J TCGA-W9-A837 
        6.71        24.16        51.06 

$`ABCA7 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       77.88        42.31         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        32.61        38.27        10.72        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77        14.40        14.40         0.23         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21         8.05        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  ABCA7 MUTATED ABCA7 WILD-TYPE 
           6.71            0.03 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
         211.17          182.33 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
          24.16           18.56 
[1] "6.7 - 211.2 (24.2)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1"  
D109V2, continuous
D109V3, binary
                 cls
clus                0   1
  ABCA7 MUTATED     3   6
  ABCA7 WILD-TYPE 204 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      3    6
  ABCA7 WILD-TYPE  204  260
        clus
vv       ABCA7 MUTATED ABCA7 WILD-TYPE
  FEMALE             3             204
  MALE               6             260
[1] 2 2
[1] FALSE
D109V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ABCA7 MUTATED             5                1                 3
  ABCA7 WILD-TYPE         170              118               176
D109V5, multiclass
                   clus
vv                  ABCA7 MUTATED ABCA7 WILD-TYPE
  ASTROCYTOMA                   5             170
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V6, binary
                 cls
clus                0   1
  ABCA7 MUTATED     2   7
  ABCA7 WILD-TYPE  90 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      2    7
  ABCA7 WILD-TYPE   90  374
     clus
vv    ABCA7 MUTATED ABCA7 WILD-TYPE
  NO              2              90
  YES             7             374
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCA7 MUTATED                                  0     0
  ABCA7 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCA7 MUTATED                           0     9
  ABCA7 WILD-TYPE                        15   429
D109V7, multiclass
                                  clus
vv                                 ABCA7 MUTATED ABCA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        9             429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V8, binary
                 cls
clus                0   1
  ABCA7 MUTATED     0   9
  ABCA7 WILD-TYPE  18 411
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      0    9
  ABCA7 WILD-TYPE   18  411
                        clus
vv                       ABCA7 MUTATED ABCA7 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             9             411
[1] 2 2
[1] FALSE

Clustering(110) Variable = FOXK1 MUTATION ANALYSIS
D110V1, survival
                 sevent
clus2               0   1
  FOXK1 MUTATED     4   0
  FOXK1 WILD-TYPE 374  93
  FOXK1 MUTATED FOXK1 WILD-TYPE 
              4             467 
  FOXK1 MUTATED FOXK1 WILD-TYPE 
              0              93 
$`FOXK1 MUTATED`
TCGA-DB-5270 TCGA-DU-5870 TCGA-HT-A5R5 TCGA-P5-A5EV 
      122.73       182.33         0.13         0.23 

$`FOXK1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R7 
       13.74        28.27        15.72         0.23        26.04        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  FOXK1 MUTATED FOXK1 WILD-TYPE 
           0.13            0.03 
  FOXK1 MUTATED FOXK1 WILD-TYPE 
         182.33          211.17 
  FOXK1 MUTATED FOXK1 WILD-TYPE 
          61.48           18.61 
[1] "0.1 - 182.3 (61.5)" "0.0 - 211.2 (18.6)"
[1] "hr="     "2.8e+07"
D110V2, continuous
D110V3, binary
                 cls
clus                0   1
  FOXK1 MUTATED     3   1
  FOXK1 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK1 MUTATED      3    1
  FOXK1 WILD-TYPE  204  265
        clus
vv       FOXK1 MUTATED FOXK1 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D110V4, continuous
[1] "Remove cluster labels:" "FOXK1 MUTATED"         
clus
  FOXK1 MUTATED FOXK1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5871      TCGA-DU-5874 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" "FOXK1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FOXK1 MUTATED             1                1                 2
  FOXK1 WILD-TYPE         174              118               177
D110V5, multiclass
                   clus
vv                  FOXK1 MUTATED FOXK1 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V6, binary
                 cls
clus                0   1
  FOXK1 MUTATED     0   4
  FOXK1 WILD-TYPE  92 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK1 MUTATED      0    4
  FOXK1 WILD-TYPE   92  377
     clus
vv    FOXK1 MUTATED FOXK1 WILD-TYPE
  NO              0              92
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXK1 MUTATED                                  0     0
  FOXK1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXK1 MUTATED                           0     4
  FOXK1 WILD-TYPE                        15   434
D110V7, multiclass
                                  clus
vv                                 FOXK1 MUTATED FOXK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V8, binary
                 cls
clus                0   1
  FOXK1 MUTATED     1   3
  FOXK1 WILD-TYPE  17 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK1 MUTATED      1    3
  FOXK1 WILD-TYPE   17  417
                        clus
vv                       FOXK1 MUTATED FOXK1 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(111) Variable = SLFN11 MUTATION ANALYSIS
D111V1, survival
                  sevent
clus2                0   1
  SLFN11 MUTATED     3   0
  SLFN11 WILD-TYPE 375  93
  SLFN11 MUTATED SLFN11 WILD-TYPE 
               3              468 
  SLFN11 MUTATED SLFN11 WILD-TYPE 
               0               93 
$`SLFN11 MUTATED`
TCGA-DU-6392 TCGA-FG-7634 TCGA-HT-7690 
      211.17        15.35         0.10 

$`SLFN11 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       24.99        23.97        18.44        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        31.69        14.96         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  SLFN11 MUTATED SLFN11 WILD-TYPE 
            0.10             0.03 
  SLFN11 MUTATED SLFN11 WILD-TYPE 
          211.17           182.33 
  SLFN11 MUTATED SLFN11 WILD-TYPE 
           15.35            18.61 
[1] "0.1 - 211.2 (15.3)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D111V2, continuous
D111V3, binary
                  cls
clus                 0   1
  SLFN11 MUTATED     1   2
  SLFN11 WILD-TYPE 206 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN11 MUTATED      1    2
  SLFN11 WILD-TYPE  206  264
        clus
vv       SLFN11 MUTATED SLFN11 WILD-TYPE
  FEMALE              1              206
  MALE                2              264
[1] 2 2
[1] FALSE
D111V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SLFN11 MUTATED             1                1                 1
  SLFN11 WILD-TYPE         174              118               178
D111V5, multiclass
                   clus
vv                  SLFN11 MUTATED SLFN11 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V6, binary
                  cls
clus                 0   1
  SLFN11 MUTATED     1   2
  SLFN11 WILD-TYPE  91 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN11 MUTATED      1    2
  SLFN11 WILD-TYPE   91  379
     clus
vv    SLFN11 MUTATED SLFN11 WILD-TYPE
  NO               1               91
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLFN11 MUTATED                                  0     0
  SLFN11 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLFN11 MUTATED                           0     3
  SLFN11 WILD-TYPE                        15   435
D111V7, multiclass
                                  clus
vv                                 SLFN11 MUTATED SLFN11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         3              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V8, binary
                  cls
clus                 0   1
  SLFN11 MUTATED     0   3
  SLFN11 WILD-TYPE  18 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN11 MUTATED      0    3
  SLFN11 WILD-TYPE   18  417
                        clus
vv                       SLFN11 MUTATED SLFN11 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              3              417
[1] 2 2
[1] FALSE

Clustering(112) Variable = MX2 MUTATION ANALYSIS
D112V1, survival
               sevent
clus2             0   1
  MX2 MUTATED     3   1
  MX2 WILD-TYPE 375  92
  MX2 MUTATED MX2 WILD-TYPE 
            4           467 
  MX2 MUTATED MX2 WILD-TYPE 
            1            92 
$`MX2 MUTATED`
TCGA-DH-A66D TCGA-HT-7616 TCGA-P5-A72U TCGA-S9-A6WL 
       27.81         0.23         0.16        31.10 

$`MX2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 
        3.16        22.06        45.99        56.09        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         1.28        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  MX2 MUTATED MX2 WILD-TYPE 
         0.16          0.03 
  MX2 MUTATED MX2 WILD-TYPE 
        31.10        211.17 
  MX2 MUTATED MX2 WILD-TYPE 
        14.02         18.61 
[1] "0.2 - 31.1 (14.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.6"
D112V2, continuous
D112V3, binary
               cls
clus              0   1
  MX2 MUTATED     2   2
  MX2 WILD-TYPE 205 264
[1] "tbl2"
               cls
clus            [,1] [,2]
  MX2 MUTATED      2    2
  MX2 WILD-TYPE  205  264
        clus
vv       MX2 MUTATED MX2 WILD-TYPE
  FEMALE           2           205
  MALE             2           264
[1] 2 2
[1] FALSE
D112V4, continuous
[1] "Remove cluster labels:" "MX2 MUTATED"           
clus
  MX2 MUTATED MX2 WILD-TYPE 
            2           267 
   TCGA-CS-4938    TCGA-CS-4941    TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-CS-5390    TCGA-CS-5393    TCGA-CS-5395    TCGA-CS-5396    TCGA-CS-5397 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-CS-6186    TCGA-CS-6188    TCGA-CS-6290    TCGA-CS-6665    TCGA-CS-6666 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-CS-6667    TCGA-CS-6668    TCGA-CS-6669    TCGA-DB-5274    TCGA-DB-A4XE 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DB-A64L    TCGA-DB-A64Q    TCGA-DB-A64R    TCGA-DB-A64S    TCGA-DB-A64U 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DB-A64V    TCGA-DB-A64W    TCGA-DB-A64X    TCGA-DB-A75L    TCGA-DB-A75O 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DH-5140    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-DH-A66B 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DH-A66F    TCGA-DH-A66G    TCGA-DH-A7UR    TCGA-DH-A7UU    TCGA-DH-A7UV 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-5851    TCGA-DU-5852    TCGA-DU-5853    TCGA-DU-5854    TCGA-DU-5855 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-5870    TCGA-DU-5871    TCGA-DU-5874    TCGA-DU-6396    TCGA-DU-6403 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-6404    TCGA-DU-6405    TCGA-DU-6407    TCGA-DU-6408    TCGA-DU-6410 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-7011    TCGA-DU-7013    TCGA-DU-7015    TCGA-DU-7018    TCGA-DU-7019 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-7294    TCGA-DU-7298    TCGA-DU-7299    TCGA-DU-7300    TCGA-DU-7301 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-7302    TCGA-DU-7304    TCGA-DU-7306    TCGA-DU-7309    TCGA-DU-8158 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-8161    TCGA-DU-8162    TCGA-DU-8163    TCGA-DU-8165    TCGA-DU-8167 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-8168    TCGA-DU-A5TP    TCGA-DU-A5TR    TCGA-DU-A5TS    TCGA-DU-A5TU 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-A5TW    TCGA-DU-A6S2    TCGA-DU-A6S6    TCGA-DU-A6S7    TCGA-DU-A6S8 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-A76R    TCGA-DU-A7T6    TCGA-DU-A7T8    TCGA-DU-A7TA    TCGA-DU-A7TB 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-DU-A7TC    TCGA-DU-A7TD    TCGA-DU-A7TG    TCGA-E1-5302    TCGA-E1-5303 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-E1-5304    TCGA-E1-5305    TCGA-E1-5307    TCGA-E1-5311    TCGA-E1-5318 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-E1-5319    TCGA-E1-5322    TCGA-E1-A7YO    TCGA-E1-A7YV    TCGA-E1-A7YW 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-E1-A7Z6    TCGA-FG-5963    TCGA-FG-5965    TCGA-FG-6688    TCGA-FG-6689 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-FG-6690    TCGA-FG-6691    TCGA-FG-7636    TCGA-FG-7638    TCGA-FG-8181 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-FG-8185    TCGA-FG-8186    TCGA-FG-8187    TCGA-FG-8188    TCGA-FG-8189 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-FG-A4MT    TCGA-FG-A4MW    TCGA-FG-A4MX    TCGA-FG-A60J    TCGA-FG-A60L 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-FG-A6J1    TCGA-FG-A6J3    TCGA-FG-A711    TCGA-FG-A713    TCGA-FG-A87Q 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-7468    TCGA-HT-7470    TCGA-HT-7475    TCGA-HT-7477    TCGA-HT-7485 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-7607    TCGA-HT-7609    TCGA-HT-7611    TCGA-HT-7689    TCGA-HT-7692 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-7693    TCGA-HT-7694    TCGA-HT-7854    TCGA-HT-7875    TCGA-HT-7884 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-8564    TCGA-HT-A4DV    TCGA-HT-A5R7    TCGA-HT-A5RA    TCGA-HT-A5RC 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-A615    TCGA-HT-A617    TCGA-HT-A618    TCGA-HT-A61A    TCGA-HT-A61B 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-HT-A61C    TCGA-HT-A74L    TCGA-IK-7675    TCGA-KT-A74X    TCGA-KT-A7W1 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-P5-A5EU    TCGA-P5-A5EV    TCGA-P5-A5EW    TCGA-P5-A5EX    TCGA-P5-A5F0 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-P5-A5F2    TCGA-P5-A5F4    TCGA-P5-A5F6    TCGA-P5-A731    TCGA-QH-A65R 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-QH-A65S    TCGA-QH-A65V    TCGA-QH-A65X    TCGA-QH-A65Z    TCGA-QH-A6CS 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-QH-A6CU    TCGA-QH-A6CV    TCGA-QH-A6CW    TCGA-QH-A6CX    TCGA-QH-A6CY 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-QH-A6CZ    TCGA-QH-A6X3    TCGA-QH-A6X4    TCGA-QH-A6X5    TCGA-QH-A6X8 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-QH-A6X9    TCGA-QH-A6XA    TCGA-QH-A6XC    TCGA-QH-A86X    TCGA-QH-A870 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-RY-A83Y    TCGA-RY-A840    TCGA-RY-A845    TCGA-RY-A847    TCGA-S9-A6TS 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A6TU    TCGA-S9-A6TV    TCGA-S9-A6TW    TCGA-S9-A6TX    TCGA-S9-A6TY 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A6TZ    TCGA-S9-A6U0    TCGA-S9-A6U1    TCGA-S9-A6U2    TCGA-S9-A6U5 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A6U6    TCGA-S9-A6U8    TCGA-S9-A6UA    TCGA-S9-A6UB    TCGA-S9-A6WD 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A6WE    TCGA-S9-A6WG    TCGA-S9-A6WH    TCGA-S9-A6WI    TCGA-S9-A6WM 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A6WN    TCGA-S9-A6WO    TCGA-S9-A6WP    TCGA-S9-A6WQ    TCGA-S9-A7IQ 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A7IS    TCGA-S9-A7IX    TCGA-S9-A7IY    TCGA-S9-A7IZ    TCGA-S9-A7J0 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A7J1    TCGA-S9-A7J2    TCGA-S9-A7J3    TCGA-S9-A7QW    TCGA-S9-A7QX 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A7QY    TCGA-S9-A7QZ    TCGA-S9-A7R1    TCGA-S9-A7R2    TCGA-S9-A7R3 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-S9-A7R4    TCGA-S9-A7R7    TCGA-S9-A7R8    TCGA-S9-A89V    TCGA-S9-A89Z 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-TM-A7C3    TCGA-TM-A7C4    TCGA-TM-A7C5    TCGA-TM-A7CA    TCGA-TM-A7CF 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-TM-A84B    TCGA-TM-A84C    TCGA-TM-A84F    TCGA-TM-A84G    TCGA-TM-A84H 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-TM-A84I    TCGA-TM-A84J    TCGA-TM-A84L    TCGA-TM-A84M    TCGA-TM-A84O 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-TM-A84Q    TCGA-TM-A84R    TCGA-TM-A84S    TCGA-TM-A84T    TCGA-TQ-A7RW 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-VM-A8C8    TCGA-VM-A8CA    TCGA-VM-A8CD    TCGA-VM-A8CE    TCGA-VM-A8CH 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" "MX2 WILD-TYPE" 
   TCGA-WY-A858    TCGA-WY-A859 
"MX2 WILD-TYPE" "MX2 WILD-TYPE" 
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MX2 MUTATED             2                0                 2
  MX2 WILD-TYPE         173              119               177
D112V5, multiclass
                   clus
vv                  MX2 MUTATED MX2 WILD-TYPE
  ASTROCYTOMA                 2           173
  OLIGOASTROCYTOMA            0           119
  OLIGODENDROGLIOMA           2           177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V6, binary
               cls
clus              0   1
  MX2 MUTATED     0   4
  MX2 WILD-TYPE  92 377
[1] "tbl2"
               cls
clus            [,1] [,2]
  MX2 MUTATED      0    4
  MX2 WILD-TYPE   92  377
     clus
vv    MX2 MUTATED MX2 WILD-TYPE
  NO            0            92
  YES           4           377
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MX2 MUTATED                                  0     0
  MX2 WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MX2 MUTATED                           0     4
  MX2 WILD-TYPE                        15   434
D112V7, multiclass
                                  clus
vv                                 MX2 MUTATED MX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                      4           434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V8, binary
               cls
clus              0   1
  MX2 MUTATED     0   4
  MX2 WILD-TYPE  18 416
[1] "tbl2"
               cls
clus            [,1] [,2]
  MX2 MUTATED      0    4
  MX2 WILD-TYPE   18  416
                        clus
vv                       MX2 MUTATED MX2 WILD-TYPE
  HISPANIC OR LATINO               0            18
  NOT HISPANIC OR LATINO           4           416
[1] 2 2
[1] FALSE

Clustering(113) Variable = SLC6A4 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  SLC6A4 MUTATED     4   0
  SLC6A4 WILD-TYPE 374  93
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
               4              467 
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
               0               93 
$`SLC6A4 MUTATED`
TCGA-DH-A7UV TCGA-DU-5871 TCGA-DU-6392 TCGA-HT-7601 
       18.61        18.94       211.17         5.03 

$`SLC6A4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.38         3.45        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 
       95.93       106.95       172.77         4.01        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
            5.03             0.03 
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
          211.17           182.33 
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
          18.775           18.610 
[1] "5.0 - 211.2 (18.8)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D113V2, continuous
D113V3, binary
                  cls
clus                 0   1
  SLC6A4 MUTATED     3   1
  SLC6A4 WILD-TYPE 204 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A4 MUTATED      3    1
  SLC6A4 WILD-TYPE  204  265
        clus
vv       SLC6A4 MUTATED SLC6A4 WILD-TYPE
  FEMALE              3              204
  MALE                1              265
[1] 2 2
[1] FALSE
D113V4, continuous
[1] "Remove cluster labels:" "SLC6A4 MUTATED"        
clus
  SLC6A4 MUTATED SLC6A4 WILD-TYPE 
               2              267 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853       TCGA-DU-5854 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5874       TCGA-DU-6396 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-6403       TCGA-DU-6404       TCGA-DU-6405       TCGA-DU-6407 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-6408       TCGA-DU-6410       TCGA-DU-7011       TCGA-DU-7013 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019       TCGA-DU-7294 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-7298       TCGA-DU-7299       TCGA-DU-7300       TCGA-DU-7301 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-7302       TCGA-DU-7304       TCGA-DU-7306       TCGA-DU-7309 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-8158       TCGA-DU-8161       TCGA-DU-8162       TCGA-DU-8163 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-8165       TCGA-DU-8167       TCGA-DU-8168       TCGA-DU-A5TP 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TU       TCGA-DU-A5TW 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-A6S2       TCGA-DU-A6S6       TCGA-DU-A6S7       TCGA-DU-A6S8 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-A76R       TCGA-DU-A7T6       TCGA-DU-A7T8       TCGA-DU-A7TA 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-DU-A7TB       TCGA-DU-A7TC       TCGA-DU-A7TD       TCGA-DU-A7TG 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5305 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5319 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-E1-5322       TCGA-E1-A7YO       TCGA-E1-A7YV       TCGA-E1-A7YW 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-E1-A7Z6       TCGA-FG-5963       TCGA-FG-5965       TCGA-FG-6688 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691       TCGA-FG-7636 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185       TCGA-FG-8186 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189       TCGA-FG-A4MT 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J       TCGA-FG-A60L 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-A6J1       TCGA-FG-A6J3       TCGA-FG-A711       TCGA-FG-A713 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470       TCGA-HT-7475 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607       TCGA-HT-7609 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692       TCGA-HT-7693 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875       TCGA-HT-7884 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7       TCGA-HT-A5RA 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617       TCGA-HT-A618 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C       TCGA-HT-A74L 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1       TCGA-P5-A5EU 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX       TCGA-P5-A5F0 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6       TCGA-P5-A731 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65X 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU       TCGA-QH-A6CV 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY       TCGA-QH-A6CZ 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5       TCGA-QH-A6X8 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC       TCGA-QH-A86X 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840       TCGA-RY-A845 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU       TCGA-S9-A6TV 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY       TCGA-S9-A6TZ 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2       TCGA-S9-A6U5 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA       TCGA-S9-A6UB 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG       TCGA-S9-A6WH 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM       TCGA-S9-A6WN 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ       TCGA-S9-A7IQ 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY       TCGA-S9-A7IZ 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2       TCGA-S9-A7J3 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY       TCGA-S9-A7QZ 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3       TCGA-S9-A7R4 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V       TCGA-S9-A89Z 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5       TCGA-TM-A7CA 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C       TCGA-TM-A84F 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I       TCGA-TM-A84J 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O       TCGA-TM-A84Q 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T       TCGA-TQ-A7RW 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD       TCGA-VM-A8CE 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
      TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" "SLC6A4 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SLC6A4 MUTATED             3                1                 0
  SLC6A4 WILD-TYPE         172              118               179
D113V5, multiclass
                   clus
vv                  SLC6A4 MUTATED SLC6A4 WILD-TYPE
  ASTROCYTOMA                    3              172
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              0              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V6, binary
                  cls
clus                 0   1
  SLC6A4 MUTATED     2   2
  SLC6A4 WILD-TYPE  90 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A4 MUTATED      2    2
  SLC6A4 WILD-TYPE   90  379
     clus
vv    SLC6A4 MUTATED SLC6A4 WILD-TYPE
  NO               2               90
  YES              2              379
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A4 MUTATED                                  0     0
  SLC6A4 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC6A4 MUTATED                           0     4
  SLC6A4 WILD-TYPE                        15   434
D113V7, multiclass
                                  clus
vv                                 SLC6A4 MUTATED SLC6A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V8, binary
                  cls
clus                 0   1
  SLC6A4 MUTATED     0   4
  SLC6A4 WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A4 MUTATED      0    4
  SLC6A4 WILD-TYPE   18  416
                        clus
vv                       SLC6A4 MUTATED SLC6A4 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(114) Variable = KRT15 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  KRT15 MUTATED     4   1
  KRT15 WILD-TYPE 374  92
  KRT15 MUTATED KRT15 WILD-TYPE 
              5             466 
  KRT15 MUTATED KRT15 WILD-TYPE 
              1              92 
$`KRT15 MUTATED`
TCGA-HT-7608 TCGA-QH-A6X9 TCGA-S9-A7R2 TCGA-TM-A7C4 TCGA-TM-A84M 
       22.06         1.91        10.39        48.33        24.79 

$`KRT15 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
       17.29         3.16        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       34.19        13.74        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        6.38        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        9.17        10.29        14.53        16.34        16.73        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       11.97        49.45        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  KRT15 MUTATED KRT15 WILD-TYPE 
           1.91            0.03 
  KRT15 MUTATED KRT15 WILD-TYPE 
          48.33          211.17 
  KRT15 MUTATED KRT15 WILD-TYPE 
          22.06           18.61 
[1] "1.9 - 48.3 (22.1)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.5"
D114V2, continuous
D114V3, binary
                 cls
clus                0   1
  KRT15 MUTATED     2   4
  KRT15 WILD-TYPE 205 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT15 MUTATED      2    4
  KRT15 WILD-TYPE  205  262
        clus
vv       KRT15 MUTATED KRT15 WILD-TYPE
  FEMALE             2             205
  MALE               4             262
[1] 2 2
[1] FALSE
D114V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  KRT15 MUTATED             3                1                 2
  KRT15 WILD-TYPE         172              118               177
D114V5, multiclass
                   clus
vv                  KRT15 MUTATED KRT15 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V6, binary
                 cls
clus                0   1
  KRT15 MUTATED     0   6
  KRT15 WILD-TYPE  92 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT15 MUTATED      0    6
  KRT15 WILD-TYPE   92  375
     clus
vv    KRT15 MUTATED KRT15 WILD-TYPE
  NO              0              92
  YES             6             375
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT15 MUTATED                                  0     0
  KRT15 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT15 MUTATED                           1     5
  KRT15 WILD-TYPE                        14   433
D114V7, multiclass
                                  clus
vv                                 KRT15 MUTATED KRT15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    1              14
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V8, binary
                 cls
clus                0   1
  KRT15 MUTATED     0   6
  KRT15 WILD-TYPE  18 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT15 MUTATED      0    6
  KRT15 WILD-TYPE   18  414
                        clus
vv                       KRT15 MUTATED KRT15 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             414
[1] 2 2
[1] FALSE

Clustering(115) Variable = F8 MUTATION ANALYSIS
D115V1, survival
              sevent
clus2            0   1
  F8 MUTATED     7   1
  F8 WILD-TYPE 371  92
  F8 MUTATED F8 WILD-TYPE 
           8          463 
  F8 MUTATED F8 WILD-TYPE 
           1           92 
$`F8 MUTATED`
TCGA-DH-A66G TCGA-DU-5852 TCGA-DU-6392 TCGA-FG-6688 TCGA-FG-A70Z TCGA-HT-7693 
       17.19         6.74       211.17        18.77        10.78        17.52 
TCGA-QH-A6CS TCGA-TM-A84H 
       19.33        30.44 

$`F8 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        27.81        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       34.36        36.82        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       22.26        28.54        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59        34.19        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       21.40         6.38        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  F8 MUTATED F8 WILD-TYPE 
        6.74         0.03 
  F8 MUTATED F8 WILD-TYPE 
      211.17       182.33 
  F8 MUTATED F8 WILD-TYPE 
      18.145       18.610 
[1] "6.7 - 211.2 (18.1)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.4"
D115V2, continuous
D115V3, binary
              cls
clus             0   1
  F8 MUTATED     7   1
  F8 WILD-TYPE 200 265
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      7    1
  F8 WILD-TYPE  200  265
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE          7          200
  MALE            1          265
[1] 2 2
[1] FALSE
D115V4, continuous
              vv
clus           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  F8 MUTATED             3                3                 2
  F8 WILD-TYPE         172              116               177
D115V5, multiclass
                   clus
vv                  F8 MUTATED F8 WILD-TYPE
  ASTROCYTOMA                3          172
  OLIGOASTROCYTOMA           3          116
  OLIGODENDROGLIOMA          2          177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V6, binary
              cls
clus             0   1
  F8 MUTATED     3   5
  F8 WILD-TYPE  89 376
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      3    5
  F8 WILD-TYPE   89  376
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO           3           89
  YES          5          376
[1] 2 2
[1] FALSE
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F8 MUTATED                                  0     0                         2
  F8 WILD-TYPE                                1     8                        13
              vv
clus           WHITE
  F8 MUTATED       6
  F8 WILD-TYPE   432
D115V7, multiclass
                                  clus
vv                                 F8 MUTATED F8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     0            8
  BLACK OR AFRICAN AMERICAN                 2           13
  WHITE                                     6          432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V8, binary
              cls
clus             0   1
  F8 MUTATED     0   8
  F8 WILD-TYPE  18 412
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      0    8
  F8 WILD-TYPE   18  412
                        clus
vv                       F8 MUTATED F8 WILD-TYPE
  HISPANIC OR LATINO              0           18
  NOT HISPANIC OR LATINO          8          412
[1] 2 2
[1] FALSE

Clustering(116) Variable = HOOK1 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  HOOK1 MUTATED     3   0
  HOOK1 WILD-TYPE 375  93
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              3             468 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              0              93 
$`HOOK1 MUTATED`
TCGA-CS-5390 TCGA-DU-6392 TCGA-S9-A89Z 
       64.64       211.17        11.97 

$`HOOK1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  HOOK1 MUTATED HOOK1 WILD-TYPE 
          11.97            0.03 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
         211.17          182.33 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          64.64           18.61 
[1] "12.0 - 211.2 (64.6)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D116V2, continuous
D116V3, binary
                 cls
clus                0   1
  HOOK1 MUTATED     2   1
  HOOK1 WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      2    1
  HOOK1 WILD-TYPE  205  265
        clus
vv       HOOK1 MUTATED HOOK1 WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D116V4, continuous
[1] "Remove cluster labels:" "HOOK1 MUTATED"         
clus
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5393      TCGA-CS-5395      TCGA-CS-5396 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188      TCGA-CS-6290 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667      TCGA-CS-6668 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE      TCGA-DB-A64L 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S      TCGA-DB-A64U 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X      TCGA-DB-A75L 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D      TCGA-DH-A66F 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU      TCGA-DH-A7UV 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5874 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HOOK1 MUTATED             2                0                 1
  HOOK1 WILD-TYPE         173              119               178
D116V5, multiclass
                   clus
vv                  HOOK1 MUTATED HOOK1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V6, binary
                 cls
clus                0   1
  HOOK1 MUTATED     2   1
  HOOK1 WILD-TYPE  90 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      2    1
  HOOK1 WILD-TYPE   90  380
     clus
vv    HOOK1 MUTATED HOOK1 WILD-TYPE
  NO              2              90
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOOK1 MUTATED                                  0     0
  HOOK1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOOK1 MUTATED                           0     3
  HOOK1 WILD-TYPE                        15   435
D116V7, multiclass
                                  clus
vv                                 HOOK1 MUTATED HOOK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V8, binary
                 cls
clus                0   1
  HOOK1 MUTATED     0   2
  HOOK1 WILD-TYPE  18 418
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      0    2
  HOOK1 WILD-TYPE   18  418
                        clus
vv                       HOOK1 MUTATED HOOK1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             2             418
[1] 2 2
[1] FALSE

Clustering(117) Variable = FMR1 MUTATION ANALYSIS
D117V1, survival
                sevent
clus2              0   1
  FMR1 MUTATED     5   0
  FMR1 WILD-TYPE 373  93
  FMR1 MUTATED FMR1 WILD-TYPE 
             5            466 
  FMR1 MUTATED FMR1 WILD-TYPE 
             0             93 
$`FMR1 MUTATED`
TCGA-DU-6392 TCGA-DU-A76O TCGA-FG-8188 TCGA-S9-A6WG TCGA-S9-A6WN 
      211.17         7.13        14.96        80.12        15.91 

$`FMR1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
        7.23         5.98        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO 
       72.59        32.45        84.99        31.10        19.86        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  FMR1 MUTATED FMR1 WILD-TYPE 
          7.13           0.03 
  FMR1 MUTATED FMR1 WILD-TYPE 
        211.17         182.33 
  FMR1 MUTATED FMR1 WILD-TYPE 
         15.91          18.61 
[1] "7.1 - 211.2 (15.9)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D117V2, continuous
D117V3, binary
                cls
clus               0   1
  FMR1 MUTATED     2   3
  FMR1 WILD-TYPE 205 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMR1 MUTATED      2    3
  FMR1 WILD-TYPE  205  263
        clus
vv       FMR1 MUTATED FMR1 WILD-TYPE
  FEMALE            2            205
  MALE              3            263
[1] 2 2
[1] FALSE
D117V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FMR1 MUTATED             4                1                 0
  FMR1 WILD-TYPE         171              118               179
D117V5, multiclass
                   clus
vv                  FMR1 MUTATED FMR1 WILD-TYPE
  ASTROCYTOMA                  4            171
  OLIGOASTROCYTOMA             1            118
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V6, binary
                cls
clus               0   1
  FMR1 MUTATED     1   4
  FMR1 WILD-TYPE  91 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMR1 MUTATED      1    4
  FMR1 WILD-TYPE   91  377
     clus
vv    FMR1 MUTATED FMR1 WILD-TYPE
  NO             1             91
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FMR1 MUTATED                                  0     0
  FMR1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FMR1 MUTATED                           0     5
  FMR1 WILD-TYPE                        15   433
D117V7, multiclass
                                  clus
vv                                 FMR1 MUTATED FMR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V8, binary
                cls
clus               0   1
  FMR1 MUTATED     0   5
  FMR1 WILD-TYPE  18 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMR1 MUTATED      0    5
  FMR1 WILD-TYPE   18  415
                        clus
vv                       FMR1 MUTATED FMR1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            415
[1] 2 2
[1] FALSE

Clustering(118) Variable = SON MUTATION ANALYSIS
D118V1, survival
               sevent
clus2             0   1
  SON MUTATED     6   2
  SON WILD-TYPE 372  91
  SON MUTATED SON WILD-TYPE 
            8           463 
  SON MUTATED SON WILD-TYPE 
            2            91 
$`SON MUTATED`
TCGA-DB-5280 TCGA-DU-5874 TCGA-DU-6392 TCGA-HT-7471 TCGA-HT-8564 TCGA-P5-A5EV 
       36.56        15.16       211.17         0.13        15.72         0.23 
TCGA-S9-A6UA TCGA-VM-A8CD 
        5.85         7.89 

$`SON WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        50.17        44.52        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       11.54        40.11         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77        14.40        14.40         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  SON MUTATED SON WILD-TYPE 
         0.13          0.03 
  SON MUTATED SON WILD-TYPE 
       211.17        182.33 
  SON MUTATED SON WILD-TYPE 
       11.525        18.710 
[1] "0.1 - 211.2 (11.5)" "0.0 - 182.3 (18.7)"
[1] "hr=" "1"  
D118V2, continuous
D118V3, binary
               cls
clus              0   1
  SON MUTATED     3   5
  SON WILD-TYPE 204 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED      3    5
  SON WILD-TYPE  204  261
        clus
vv       SON MUTATED SON WILD-TYPE
  FEMALE           3           204
  MALE             5           261
[1] 2 2
[1] FALSE
D118V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SON MUTATED             5                1                 2
  SON WILD-TYPE         170              118               177
D118V5, multiclass
                   clus
vv                  SON MUTATED SON WILD-TYPE
  ASTROCYTOMA                 5           170
  OLIGOASTROCYTOMA            1           118
  OLIGODENDROGLIOMA           2           177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V6, binary
               cls
clus              0   1
  SON MUTATED     1   7
  SON WILD-TYPE  91 374
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED      1    7
  SON WILD-TYPE   91  374
     clus
vv    SON MUTATED SON WILD-TYPE
  NO            1            91
  YES           7           374
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SON MUTATED                                  0     0
  SON WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SON MUTATED                           0     8
  SON WILD-TYPE                        15   430
D118V7, multiclass
                                  clus
vv                                 SON MUTATED SON WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             8
  BLACK OR AFRICAN AMERICAN                  0            15
  WHITE                                      8           430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V8, binary
               cls
clus              0   1
  SON MUTATED     1   6
  SON WILD-TYPE  17 414
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED      1    6
  SON WILD-TYPE   17  414
                        clus
vv                       SON MUTATED SON WILD-TYPE
  HISPANIC OR LATINO               1            17
  NOT HISPANIC OR LATINO           6           414
[1] 2 2
[1] FALSE

Clustering(119) Variable = TTC30B MUTATION ANALYSIS
D119V1, survival
                  sevent
clus2                0   1
  TTC30B MUTATED     5   1
  TTC30B WILD-TYPE 373  92
  TTC30B MUTATED TTC30B WILD-TYPE 
               6              465 
  TTC30B MUTATED TTC30B WILD-TYPE 
               1               92 
$`TTC30B MUTATED`
TCGA-DU-6392 TCGA-DU-A7T8 TCGA-S9-A6TX TCGA-TM-A84L TCGA-TM-A84Q TCGA-WY-A859 
      211.17       124.50        34.49        40.83        25.38        39.88 

$`TTC30B WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
       17.98        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.16        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        13.32        43.96        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  TTC30B MUTATED TTC30B WILD-TYPE 
           25.38             0.03 
  TTC30B MUTATED TTC30B WILD-TYPE 
          211.17           182.33 
  TTC30B MUTATED TTC30B WILD-TYPE 
          40.355           18.440 
[1] "25.4 - 211.2 (40.4)" "0.0 - 182.3 (18.4)" 
[1] "hr=" "3.7"
D119V2, continuous
D119V3, binary
                  cls
clus                 0   1
  TTC30B MUTATED     2   4
  TTC30B WILD-TYPE 205 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC30B MUTATED      2    4
  TTC30B WILD-TYPE  205  262
        clus
vv       TTC30B MUTATED TTC30B WILD-TYPE
  FEMALE              2              205
  MALE                4              262
[1] 2 2
[1] FALSE
D119V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TTC30B MUTATED             3                2                 1
  TTC30B WILD-TYPE         172              117               178
D119V5, multiclass
                   clus
vv                  TTC30B MUTATED TTC30B WILD-TYPE
  ASTROCYTOMA                    3              172
  OLIGOASTROCYTOMA               2              117
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V6, binary
                  cls
clus                 0   1
  TTC30B MUTATED     1   5
  TTC30B WILD-TYPE  91 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC30B MUTATED      1    5
  TTC30B WILD-TYPE   91  376
     clus
vv    TTC30B MUTATED TTC30B WILD-TYPE
  NO               1               91
  YES              5              376
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTC30B MUTATED                                  0     0
  TTC30B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TTC30B MUTATED                           0     6
  TTC30B WILD-TYPE                        15   432
D119V7, multiclass
                                  clus
vv                                 TTC30B MUTATED TTC30B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         6              432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V8, binary
                  cls
clus                 0   1
  TTC30B MUTATED     0   5
  TTC30B WILD-TYPE  18 415
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC30B MUTATED      0    5
  TTC30B WILD-TYPE   18  415
                        clus
vv                       TTC30B MUTATED TTC30B WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              5              415
[1] 2 2
[1] FALSE

Clustering(120) Variable = FANCD2 MUTATION ANALYSIS
D120V1, survival
                  sevent
clus2                0   1
  FANCD2 MUTATED     6   1
  FANCD2 WILD-TYPE 372  92
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              464 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               1               92 
$`FANCD2 MUTATED`
TCGA-DB-A64O TCGA-DU-6392 TCGA-FG-5964 TCGA-FG-A4MY TCGA-FG-A713 TCGA-P5-A72W 
       25.48       211.17        34.36        23.70        20.45        10.42 
TCGA-RY-A83Z 
        9.90 

$`FANCD2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87N 
       22.26        28.54        10.78        36.66        48.69        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59        34.19        13.74        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         1.28         0.16        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  FANCD2 MUTATED FANCD2 WILD-TYPE 
            9.90             0.03 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
          211.17           182.33 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           23.70            18.56 
[1] "9.9 - 211.2 (23.7)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2.5"
D120V2, continuous
D120V3, binary
                  cls
clus                 0   1
  FANCD2 MUTATED     4   3
  FANCD2 WILD-TYPE 203 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      4    3
  FANCD2 WILD-TYPE  203  263
        clus
vv       FANCD2 MUTATED FANCD2 WILD-TYPE
  FEMALE              4              203
  MALE                3              263
[1] 2 2
[1] FALSE
D120V4, continuous
[1] "Remove cluster labels:" "FANCD2 MUTATED"        
clus
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A87Q       TCGA-HT-7468       TCGA-HT-7470 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485       TCGA-HT-7607 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689       TCGA-HT-7692 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854       TCGA-HT-7875 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV       TCGA-HT-A5R7 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615       TCGA-HT-A617 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B       TCGA-HT-A61C 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X       TCGA-KT-A7W1 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S       TCGA-QH-A65V 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS       TCGA-QH-A6CU 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX       TCGA-QH-A6CY 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4       TCGA-QH-A6X5 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA       TCGA-QH-A6XC 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y       TCGA-RY-A840 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TS       TCGA-S9-A6TU 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" "FANCD2 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FANCD2 MUTATED             3                3                 1
  FANCD2 WILD-TYPE         172              116               178
D120V5, multiclass
                   clus
vv                  FANCD2 MUTATED FANCD2 WILD-TYPE
  ASTROCYTOMA                    3              172
  OLIGOASTROCYTOMA               3              116
  OLIGODENDROGLIOMA              1              178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V6, binary
                  cls
clus                 0   1
  FANCD2 MUTATED     2   5
  FANCD2 WILD-TYPE  90 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      2    5
  FANCD2 WILD-TYPE   90  376
     clus
vv    FANCD2 MUTATED FANCD2 WILD-TYPE
  NO               2               90
  YES              5              376
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FANCD2 MUTATED                                  0     0
  FANCD2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FANCD2 MUTATED                           0     7
  FANCD2 WILD-TYPE                        15   431
D120V7, multiclass
                                  clus
vv                                 FANCD2 MUTATED FANCD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         7              431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V8, binary
                  cls
clus                 0   1
  FANCD2 MUTATED     1   6
  FANCD2 WILD-TYPE  17 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      1    6
  FANCD2 WILD-TYPE   17  414
                        clus
vv                       FANCD2 MUTATED FANCD2 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              6              414
[1] 2 2
[1] FALSE

Clustering(121) Variable = RGL2 MUTATION ANALYSIS
D121V1, survival
                sevent
clus2              0   1
  RGL2 MUTATED     4   0
  RGL2 WILD-TYPE 374  93
  RGL2 MUTATED RGL2 WILD-TYPE 
             4            467 
  RGL2 MUTATED RGL2 WILD-TYPE 
             0             93 
$`RGL2 MUTATED`
TCGA-DH-A66B TCGA-DU-6392 TCGA-DU-8167 TCGA-S9-A6WL 
       42.05       211.17        15.48        31.10 

$`RGL2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 
       14.60        20.68        21.40        19.13        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  RGL2 MUTATED RGL2 WILD-TYPE 
         15.48           0.03 
  RGL2 MUTATED RGL2 WILD-TYPE 
        211.17         182.33 
  RGL2 MUTATED RGL2 WILD-TYPE 
        36.575         18.610 
[1] "15.5 - 211.2 (36.6)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D121V2, continuous
D121V3, binary
                cls
clus               0   1
  RGL2 MUTATED     2   2
  RGL2 WILD-TYPE 205 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED      2    2
  RGL2 WILD-TYPE  205  264
        clus
vv       RGL2 MUTATED RGL2 WILD-TYPE
  FEMALE            2            205
  MALE              2            264
[1] 2 2
[1] FALSE
D121V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RGL2 MUTATED             3                1                 0
  RGL2 WILD-TYPE         172              118               179
D121V5, multiclass
                   clus
vv                  RGL2 MUTATED RGL2 WILD-TYPE
  ASTROCYTOMA                  3            172
  OLIGOASTROCYTOMA             1            118
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V6, binary
                cls
clus               0   1
  RGL2 MUTATED     1   3
  RGL2 WILD-TYPE  91 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED      1    3
  RGL2 WILD-TYPE   91  378
     clus
vv    RGL2 MUTATED RGL2 WILD-TYPE
  NO             1             91
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGL2 MUTATED                                  0     0
  RGL2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RGL2 MUTATED                           0     4
  RGL2 WILD-TYPE                        15   434
D121V7, multiclass
                                  clus
vv                                 RGL2 MUTATED RGL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       4            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V8, binary
                cls
clus               0   1
  RGL2 MUTATED     0   4
  RGL2 WILD-TYPE  18 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED      0    4
  RGL2 WILD-TYPE   18  416
                        clus
vv                       RGL2 MUTATED RGL2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE

Clustering(122) Variable = NR1H3 MUTATION ANALYSIS
D122V1, survival
                 sevent
clus2               0   1
  NR1H3 MUTATED     4   0
  NR1H3 WILD-TYPE 374  93
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              4             467 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              0              93 
$`NR1H3 MUTATED`
TCGA-DU-6392 TCGA-FG-8186 TCGA-HT-7686 TCGA-S9-A6U0 
      211.17        16.01        42.74        22.95 

$`NR1H3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  NR1H3 MUTATED NR1H3 WILD-TYPE 
          16.01            0.03 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
         211.17          182.33 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
         32.845          18.610 
[1] "16.0 - 211.2 (32.8)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D122V2, continuous
D122V3, binary
                 cls
clus                0   1
  NR1H3 MUTATED     3   1
  NR1H3 WILD-TYPE 204 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED      3    1
  NR1H3 WILD-TYPE  204  265
        clus
vv       NR1H3 MUTATED NR1H3 WILD-TYPE
  FEMALE             3             204
  MALE               1             265
[1] 2 2
[1] FALSE
D122V4, continuous
[1] "Remove cluster labels:" "NR1H3 MUTATED"         
clus
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" "NR1H3 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NR1H3 MUTATED             3                1                 0
  NR1H3 WILD-TYPE         172              118               179
D122V5, multiclass
                   clus
vv                  NR1H3 MUTATED NR1H3 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V6, binary
                 cls
clus                0   1
  NR1H3 MUTATED     2   2
  NR1H3 WILD-TYPE  90 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED      2    2
  NR1H3 WILD-TYPE   90  379
     clus
vv    NR1H3 MUTATED NR1H3 WILD-TYPE
  NO              2              90
  YES             2             379
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR1H3 MUTATED                                  0     0
  NR1H3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR1H3 MUTATED                           0     4
  NR1H3 WILD-TYPE                        15   434
D122V7, multiclass
                                  clus
vv                                 NR1H3 MUTATED NR1H3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V8, binary
                 cls
clus                0   1
  NR1H3 MUTATED     1   3
  NR1H3 WILD-TYPE  17 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED      1    3
  NR1H3 WILD-TYPE   17  417
                        clus
vv                       NR1H3 MUTATED NR1H3 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(123) Variable = TYRP1 MUTATION ANALYSIS
D123V1, survival
                 sevent
clus2               0   1
  TYRP1 MUTATED     3   1
  TYRP1 WILD-TYPE 375  92
  TYRP1 MUTATED TYRP1 WILD-TYPE 
              4             467 
  TYRP1 MUTATED TYRP1 WILD-TYPE 
              1              92 
$`TYRP1 MUTATED`
TCGA-DU-6392 TCGA-DU-6405 TCGA-HT-A614 TCGA-S9-A6WL 
      211.17        19.89         2.70        31.10 

$`TYRP1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
       20.22         0.07        27.35         0.10         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  TYRP1 MUTATED TYRP1 WILD-TYPE 
           2.70            0.03 
  TYRP1 MUTATED TYRP1 WILD-TYPE 
         211.17          182.33 
  TYRP1 MUTATED TYRP1 WILD-TYPE 
         25.495          18.610 
[1] "2.7 - 211.2 (25.5)" "0.0 - 182.3 (18.6)"
[1] "hr=" "2"  
D123V2, continuous
D123V3, binary
                 cls
clus                0   1
  TYRP1 MUTATED     2   2
  TYRP1 WILD-TYPE 205 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRP1 MUTATED      2    2
  TYRP1 WILD-TYPE  205  264
        clus
vv       TYRP1 MUTATED TYRP1 WILD-TYPE
  FEMALE             2             205
  MALE               2             264
[1] 2 2
[1] FALSE
D123V4, continuous
[1] "Remove cluster labels:" "TYRP1 MUTATED"         
clus
  TYRP1 MUTATED TYRP1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WM      TCGA-S9-A6WN 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" "TYRP1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TYRP1 MUTATED             3                1                 0
  TYRP1 WILD-TYPE         172              118               179
D123V5, multiclass
                   clus
vv                  TYRP1 MUTATED TYRP1 WILD-TYPE
  ASTROCYTOMA                   3             172
  OLIGOASTROCYTOMA              1             118
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V6, binary
                 cls
clus                0   1
  TYRP1 MUTATED     2   2
  TYRP1 WILD-TYPE  90 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRP1 MUTATED      2    2
  TYRP1 WILD-TYPE   90  379
     clus
vv    TYRP1 MUTATED TYRP1 WILD-TYPE
  NO              2              90
  YES             2             379
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TYRP1 MUTATED                                  0     0
  TYRP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TYRP1 MUTATED                           0     4
  TYRP1 WILD-TYPE                        15   434
D123V7, multiclass
                                  clus
vv                                 TYRP1 MUTATED TYRP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V8, binary
                 cls
clus                0   1
  TYRP1 MUTATED     0   4
  TYRP1 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRP1 MUTATED      0    4
  TYRP1 WILD-TYPE   18  416
                        clus
vv                       TYRP1 MUTATED TYRP1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(124) Variable = SLC25A5 MUTATION ANALYSIS
D124V1, survival
                   sevent
clus2                 0   1
  SLC25A5 MUTATED     1   3
  SLC25A5 WILD-TYPE 377  90
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
                4               467 
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
                3                90 
$`SLC25A5 MUTATED`
TCGA-CS-5395 TCGA-E1-A7Z6 TCGA-FG-A711 TCGA-FG-A713 
       21.01        32.35        48.69        20.45 

$`SLC25A5 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       32.45        36.82        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
            20.45              0.03 
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
            48.69            211.17 
  SLC25A5 MUTATED SLC25A5 WILD-TYPE 
            26.68             18.51 
[1] "20.4 - 48.7 (26.7)" "0.0 - 211.2 (18.5)"
[1] "hr=" "3.8"
D124V2, continuous
D124V3, binary
                   cls
clus                  0   1
  SLC25A5 MUTATED     3   1
  SLC25A5 WILD-TYPE 204 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC25A5 MUTATED      3    1
  SLC25A5 WILD-TYPE  204  265
        clus
vv       SLC25A5 MUTATED SLC25A5 WILD-TYPE
  FEMALE               3               204
  MALE                 1               265
[1] 2 2
[1] FALSE
D124V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SLC25A5 MUTATED             1                1                 2
  SLC25A5 WILD-TYPE         174              118               177
D124V5, multiclass
                   clus
vv                  SLC25A5 MUTATED SLC25A5 WILD-TYPE
  ASTROCYTOMA                     1               174
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               2               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V6, binary
                   cls
clus                  0   1
  SLC25A5 MUTATED     1   3
  SLC25A5 WILD-TYPE  91 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC25A5 MUTATED      1    3
  SLC25A5 WILD-TYPE   91  378
     clus
vv    SLC25A5 MUTATED SLC25A5 WILD-TYPE
  NO                1                91
  YES               3               378
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A5 MUTATED                                  0     0
  SLC25A5 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC25A5 MUTATED                           1     3
  SLC25A5 WILD-TYPE                        14   435
D124V7, multiclass
                                  clus
vv                                 SLC25A5 MUTATED SLC25A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          3               435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V8, binary
                   cls
clus                  0   1
  SLC25A5 MUTATED     0   3
  SLC25A5 WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC25A5 MUTATED      0    3
  SLC25A5 WILD-TYPE   18  417
                        clus
vv                       SLC25A5 MUTATED SLC25A5 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               417
[1] 2 2
[1] FALSE

Clustering(125) Variable = AGBL1 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  AGBL1 MUTATED     4   0
  AGBL1 WILD-TYPE 374  93
  AGBL1 MUTATED AGBL1 WILD-TYPE 
              4             467 
  AGBL1 MUTATED AGBL1 WILD-TYPE 
              0              93 
$`AGBL1 MUTATED`
TCGA-DB-A4XA TCGA-FG-A4MU TCGA-HT-8106 TCGA-RY-A83Z 
       18.84        10.72         0.10         9.90 

$`AGBL1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AGBL1 MUTATED AGBL1 WILD-TYPE 
           0.10            0.03 
  AGBL1 MUTATED AGBL1 WILD-TYPE 
          18.84          211.17 
  AGBL1 MUTATED AGBL1 WILD-TYPE 
          10.31           18.61 
[1] "0.1 - 18.8 (10.3)"  "0.0 - 211.2 (18.6)"
[1] "hr="     "1200000"
D125V2, continuous
D125V3, binary
                 cls
clus                0   1
  AGBL1 MUTATED     1   3
  AGBL1 WILD-TYPE 206 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL1 MUTATED      1    3
  AGBL1 WILD-TYPE  206  263
        clus
vv       AGBL1 MUTATED AGBL1 WILD-TYPE
  FEMALE             1             206
  MALE               3             263
[1] 2 2
[1] FALSE
D125V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AGBL1 MUTATED             2                2                 0
  AGBL1 WILD-TYPE         173              117               179
D125V5, multiclass
                   clus
vv                  AGBL1 MUTATED AGBL1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              2             117
  OLIGODENDROGLIOMA             0             179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V6, binary
                 cls
clus                0   1
  AGBL1 MUTATED     0   4
  AGBL1 WILD-TYPE  92 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL1 MUTATED      0    4
  AGBL1 WILD-TYPE   92  377
     clus
vv    AGBL1 MUTATED AGBL1 WILD-TYPE
  NO              0              92
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGBL1 MUTATED                                  0     0
  AGBL1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGBL1 MUTATED                           0     4
  AGBL1 WILD-TYPE                        15   434
D125V7, multiclass
                                  clus
vv                                 AGBL1 MUTATED AGBL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V8, binary
                 cls
clus                0   1
  AGBL1 MUTATED     0   4
  AGBL1 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL1 MUTATED      0    4
  AGBL1 WILD-TYPE   18  416
                        clus
vv                       AGBL1 MUTATED AGBL1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(126) Variable = AMPD1 MUTATION ANALYSIS
D126V1, survival
                 sevent
clus2               0   1
  AMPD1 MUTATED     2   2
  AMPD1 WILD-TYPE 376  91
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              4             467 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              2              91 
$`AMPD1 MUTATED`
TCGA-DU-6392 TCGA-DU-A76K TCGA-FG-A711 TCGA-TM-A84Q 
      211.17        11.41        48.69        25.38 

$`AMPD1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        7.23         5.98        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMPD1 MUTATED AMPD1 WILD-TYPE 
          11.41            0.03 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
         211.17          182.33 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
         37.035          18.610 
[1] "11.4 - 211.2 (37.0)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "1.1"
D126V2, continuous
D126V3, binary
                 cls
clus                0   1
  AMPD1 MUTATED     2   2
  AMPD1 WILD-TYPE 205 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      2    2
  AMPD1 WILD-TYPE  205  264
        clus
vv       AMPD1 MUTATED AMPD1 WILD-TYPE
  FEMALE             2             205
  MALE               2             264
[1] 2 2
[1] FALSE
D126V4, continuous
[1] "Remove cluster labels:" "AMPD1 MUTATED"         
clus
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" "AMPD1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMPD1 MUTATED             2                0                 2
  AMPD1 WILD-TYPE         173              119               177
D126V5, multiclass
                   clus
vv                  AMPD1 MUTATED AMPD1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V6, binary
                 cls
clus                0   1
  AMPD1 MUTATED     1   3
  AMPD1 WILD-TYPE  91 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      1    3
  AMPD1 WILD-TYPE   91  378
     clus
vv    AMPD1 MUTATED AMPD1 WILD-TYPE
  NO              1              91
  YES             3             378
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMPD1 MUTATED                                  0     0
  AMPD1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AMPD1 MUTATED                           0     4
  AMPD1 WILD-TYPE                        15   434
D126V7, multiclass
                                  clus
vv                                 AMPD1 MUTATED AMPD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V8, binary
                 cls
clus                0   1
  AMPD1 MUTATED     0   4
  AMPD1 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      0    4
  AMPD1 WILD-TYPE   18  416
                        clus
vv                       AMPD1 MUTATED AMPD1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(127) Variable = NGEF MUTATION ANALYSIS
D127V1, survival
                sevent
clus2              0   1
  NGEF MUTATED     4   1
  NGEF WILD-TYPE 374  92
  NGEF MUTATED NGEF WILD-TYPE 
             5            466 
  NGEF MUTATED NGEF WILD-TYPE 
             1             92 
$`NGEF MUTATED`
TCGA-DU-6392 TCGA-FG-8186 TCGA-IK-8125 TCGA-TM-A84H TCGA-TQ-A7RW 
      211.17        16.01        42.77        30.44        26.99 

$`NGEF WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        19.00        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       23.80        15.98        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  NGEF MUTATED NGEF WILD-TYPE 
         16.01           0.03 
  NGEF MUTATED NGEF WILD-TYPE 
        211.17         182.33 
  NGEF MUTATED NGEF WILD-TYPE 
         30.44          18.56 
[1] "16.0 - 211.2 (30.4)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.5"
D127V2, continuous
D127V3, binary
                cls
clus               0   1
  NGEF MUTATED     3   2
  NGEF WILD-TYPE 204 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED      3    2
  NGEF WILD-TYPE  204  264
        clus
vv       NGEF MUTATED NGEF WILD-TYPE
  FEMALE            3            204
  MALE              2            264
[1] 2 2
[1] FALSE
D127V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NGEF MUTATED             1                3                 1
  NGEF WILD-TYPE         174              116               178
D127V5, multiclass
                   clus
vv                  NGEF MUTATED NGEF WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            1            178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V6, binary
                cls
clus               0   1
  NGEF MUTATED     1   4
  NGEF WILD-TYPE  91 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED      1    4
  NGEF WILD-TYPE   91  377
     clus
vv    NGEF MUTATED NGEF WILD-TYPE
  NO             1             91
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NGEF MUTATED                                  0     0
  NGEF WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NGEF MUTATED                           0     5
  NGEF WILD-TYPE                        15   433
D127V7, multiclass
                                  clus
vv                                 NGEF MUTATED NGEF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V8, binary
                cls
clus               0   1
  NGEF MUTATED     2   3
  NGEF WILD-TYPE  16 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED      2    3
  NGEF WILD-TYPE   16  417
                        clus
vv                       NGEF MUTATED NGEF WILD-TYPE
  HISPANIC OR LATINO                2             16
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(128) Variable = YIPF1 MUTATION ANALYSIS
D128V1, survival
                 sevent
clus2               0   1
  YIPF1 MUTATED     3   0
  YIPF1 WILD-TYPE 375  93
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             468 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              0              93 
$`YIPF1 MUTATED`
TCGA-DU-6392 TCGA-EZ-7264 TCGA-HT-7884 
      211.17        14.33        11.28 

$`YIPF1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       32.45        36.82        32.35         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 
        0.13         3.68         5.33        35.47         3.72        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  YIPF1 MUTATED YIPF1 WILD-TYPE 
          11.28            0.03 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
         211.17          182.33 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
          14.33           18.61 
[1] "11.3 - 211.2 (14.3)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D128V2, continuous
D128V3, binary
                 cls
clus                0   1
  YIPF1 MUTATED     3   0
  YIPF1 WILD-TYPE 204 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      3    0
  YIPF1 WILD-TYPE  204  266
        clus
vv       YIPF1 MUTATED YIPF1 WILD-TYPE
  FEMALE             3             204
  MALE               0             266
[1] 2 2
[1] FALSE
D128V4, continuous
[1] "Remove cluster labels:" "YIPF1 MUTATED"         
clus
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-FG-A711      TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-7875      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  YIPF1 MUTATED             2                0                 1
  YIPF1 WILD-TYPE         173              119               178
D128V5, multiclass
                   clus
vv                  YIPF1 MUTATED YIPF1 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V6, binary
                 cls
clus                0   1
  YIPF1 MUTATED     1   2
  YIPF1 WILD-TYPE  91 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      1    2
  YIPF1 WILD-TYPE   91  379
     clus
vv    YIPF1 MUTATED YIPF1 WILD-TYPE
  NO              1              91
  YES             2             379
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YIPF1 MUTATED                                  0     0
  YIPF1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YIPF1 MUTATED                           0     3
  YIPF1 WILD-TYPE                        15   435
D128V7, multiclass
                                  clus
vv                                 YIPF1 MUTATED YIPF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V8, binary
                 cls
clus                0   1
  YIPF1 MUTATED     0   3
  YIPF1 WILD-TYPE  18 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      0    3
  YIPF1 WILD-TYPE   18  417
                        clus
vv                       YIPF1 MUTATED YIPF1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(129) Variable = PDHA1 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  PDHA1 MUTATED     3   2
  PDHA1 WILD-TYPE 375  91
  PDHA1 MUTATED PDHA1 WILD-TYPE 
              5             466 
  PDHA1 MUTATED PDHA1 WILD-TYPE 
              2              91 
$`PDHA1 MUTATED`
TCGA-DB-A4XH TCGA-DU-5854 TCGA-E1-5318 TCGA-E1-5322 TCGA-QH-A6X5 
       31.63         8.45        78.21       130.78        16.34 

$`PDHA1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
      134.27        95.57        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  PDHA1 MUTATED PDHA1 WILD-TYPE 
           8.45            0.03 
  PDHA1 MUTATED PDHA1 WILD-TYPE 
         130.78          211.17 
  PDHA1 MUTATED PDHA1 WILD-TYPE 
          31.63           18.61 
[1] "8.4 - 130.8 (31.6)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1"  
D129V2, continuous
D129V3, binary
                 cls
clus                0   1
  PDHA1 MUTATED     5   0
  PDHA1 WILD-TYPE 202 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDHA1 MUTATED      5    0
  PDHA1 WILD-TYPE  202  266
        clus
vv       PDHA1 MUTATED PDHA1 WILD-TYPE
  FEMALE             5             202
  MALE               0             266
[1] 2 2
[1] FALSE
D129V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PDHA1 MUTATED             1                3                 1
  PDHA1 WILD-TYPE         174              116               178
D129V5, multiclass
                   clus
vv                  PDHA1 MUTATED PDHA1 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              3             116
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V6, binary
                 cls
clus                0   1
  PDHA1 MUTATED     1   4
  PDHA1 WILD-TYPE  91 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDHA1 MUTATED      1    4
  PDHA1 WILD-TYPE   91  377
     clus
vv    PDHA1 MUTATED PDHA1 WILD-TYPE
  NO              1              91
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDHA1 MUTATED                                  0     0
  PDHA1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDHA1 MUTATED                           0     5
  PDHA1 WILD-TYPE                        15   433
D129V7, multiclass
                                  clus
vv                                 PDHA1 MUTATED PDHA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        5             433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V8, binary
                 cls
clus                0   1
  PDHA1 MUTATED     0   5
  PDHA1 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDHA1 MUTATED      0    5
  PDHA1 WILD-TYPE   18  415
                        clus
vv                       PDHA1 MUTATED PDHA1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(130) Variable = ASXL2 MUTATION ANALYSIS
D130V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED     3   0
  ASXL2 WILD-TYPE 375  93
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              3             468 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              0              93 
$`ASXL2 MUTATED`
TCGA-DU-6392 TCGA-FG-7638 TCGA-S9-A7J1 
      211.17        22.55         8.19 

$`ASXL2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J2 
        7.92        22.32        23.51         7.13        20.02         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           8.19            0.03 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         211.17          182.33 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
          22.55           18.61 
[1] "8.2 - 211.2 (22.6)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D130V2, continuous
D130V3, binary
                 cls
clus                0   1
  ASXL2 MUTATED     2   1
  ASXL2 WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      2    1
  ASXL2 WILD-TYPE  205  265
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D130V4, continuous
[1] "Remove cluster labels:" "ASXL2 MUTATED"         
clus
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-A6S7      TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-A7T8      TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DU-A7TD      TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-E1-A7YV      TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-8181      TCGA-FG-8185 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J2      TCGA-S9-A7J3 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ASXL2 MUTATED             1                0                 2
  ASXL2 WILD-TYPE         174              119               177
D130V5, multiclass
                   clus
vv                  ASXL2 MUTATED ASXL2 WILD-TYPE
  ASTROCYTOMA                   1             174
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V6, binary
                 cls
clus                0   1
  ASXL2 MUTATED     2   1
  ASXL2 WILD-TYPE  90 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      2    1
  ASXL2 WILD-TYPE   90  380
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO              2              90
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL2 MUTATED                                  0     0
  ASXL2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED                           0     3
  ASXL2 WILD-TYPE                        15   435
D130V7, multiclass
                                  clus
vv                                 ASXL2 MUTATED ASXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V8, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0   3
  ASXL2 WILD-TYPE  18 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0    3
  ASXL2 WILD-TYPE   18  417
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(131) Variable = HLA-DRA MUTATION ANALYSIS
D131V1, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED     2   1
  HLA-DRA WILD-TYPE 376  92
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                3               468 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                1                92 
$`HLA-DRA MUTATED`
TCGA-CS-4942 TCGA-DU-6392 TCGA-FG-A6J3 
       43.89       211.17        22.26 

$`HLA-DRA WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            22.26              0.03 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           211.17            182.33 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            43.89             18.56 
[1] "22.3 - 211.2 (43.9)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.1"
D131V2, continuous
D131V3, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     3   0
  HLA-DRA WILD-TYPE 204 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      3    0
  HLA-DRA WILD-TYPE  204  266
        clus
vv       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  FEMALE               3               204
  MALE                 0               266
[1] 2 2
[1] FALSE
D131V4, continuous
[1] "Remove cluster labels:" "HLA-DRA MUTATED"       
clus
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                2               267 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4943        TCGA-CS-4944 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395        TCGA-CS-5396 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6290 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667        TCGA-CS-6668 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE        TCGA-DB-A64L 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S        TCGA-DB-A64U 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X        TCGA-DB-A75L 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142        TCGA-DH-5143 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D        TCGA-DH-A66F 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU        TCGA-DH-A7UV 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853        TCGA-DU-5854 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871        TCGA-DU-5874 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-7011 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299        TCGA-DU-7300 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304        TCGA-DU-7306 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161        TCGA-DU-8162 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167        TCGA-DU-8168 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TU 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6        TCGA-DU-A6S7 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6        TCGA-DU-A7T8 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC        TCGA-DU-A7TD 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YO        TCGA-E1-A7YV 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-E1-A7YW        TCGA-E1-A7Z6        TCGA-FG-5963        TCGA-FG-5965 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181        TCGA-FG-8185 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A60J 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A711        TCGA-FG-A713 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-FG-A87Q        TCGA-HT-7468        TCGA-HT-7470        TCGA-HT-7475 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7485        TCGA-HT-7607        TCGA-HT-7609 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-7611        TCGA-HT-7689        TCGA-HT-7692        TCGA-HT-7693 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7875        TCGA-HT-7884 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R7        TCGA-HT-A5RA 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617        TCGA-HT-A618 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-HT-A61A        TCGA-HT-A61B        TCGA-HT-A61C        TCGA-HT-A74L 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1        TCGA-P5-A5EU 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5F0 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6        TCGA-P5-A731 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-QH-A870        TCGA-RY-A83Y        TCGA-RY-A840        TCGA-RY-A845 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-RY-A847        TCGA-S9-A6TS        TCGA-S9-A6TU        TCGA-S9-A6TV 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6TW        TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6U6        TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T        TCGA-TQ-A7RW 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
       TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" "HLA-DRA WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HLA-DRA MUTATED             3                0                 0
  HLA-DRA WILD-TYPE         172              119               179
D131V5, multiclass
                   clus
vv                  HLA-DRA MUTATED HLA-DRA WILD-TYPE
  ASTROCYTOMA                     3               172
  OLIGOASTROCYTOMA                0               119
  OLIGODENDROGLIOMA               0               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V6, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     2   1
  HLA-DRA WILD-TYPE  90 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      2    1
  HLA-DRA WILD-TYPE   90  380
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  NO                2                90
  YES               1               380
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-DRA MUTATED                                  0     0
  HLA-DRA WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HLA-DRA MUTATED                           1     2
  HLA-DRA WILD-TYPE                        14   436
D131V7, multiclass
                                  clus
vv                                 HLA-DRA MUTATED HLA-DRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          2               436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V8, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     0   2
  HLA-DRA WILD-TYPE  18 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      0    2
  HLA-DRA WILD-TYPE   18  418
                        clus
vv                       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               2               418
[1] 2 2
[1] FALSE

Clustering(132) Variable = ALPP MUTATION ANALYSIS
D132V1, survival
                sevent
clus2              0   1
  ALPP MUTATED     4   0
  ALPP WILD-TYPE 374  93
  ALPP MUTATED ALPP WILD-TYPE 
             4            467 
  ALPP MUTATED ALPP WILD-TYPE 
             0             93 
$`ALPP MUTATED`
TCGA-CS-5390 TCGA-FG-A4MY TCGA-HT-A617 TCGA-QH-A65S 
       64.64        23.70        16.14         2.53 

$`ALPP WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
       16.93         1.81        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  ALPP MUTATED ALPP WILD-TYPE 
          2.53           0.03 
  ALPP MUTATED ALPP WILD-TYPE 
         64.64         211.17 
  ALPP MUTATED ALPP WILD-TYPE 
         19.92          18.61 
[1] "2.5 - 64.6 (19.9)"  "0.0 - 211.2 (18.6)"
[1] "hr="     "3300000"
D132V2, continuous
D132V3, binary
                cls
clus               0   1
  ALPP MUTATED     3   1
  ALPP WILD-TYPE 204 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      3    1
  ALPP WILD-TYPE  204  265
        clus
vv       ALPP MUTATED ALPP WILD-TYPE
  FEMALE            3            204
  MALE              1            265
[1] 2 2
[1] FALSE
D132V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ALPP MUTATED             0                2                 2
  ALPP WILD-TYPE         175              117               177
D132V5, multiclass
                   clus
vv                  ALPP MUTATED ALPP WILD-TYPE
  ASTROCYTOMA                  0            175
  OLIGOASTROCYTOMA             2            117
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V6, binary
                cls
clus               0   1
  ALPP MUTATED     1   3
  ALPP WILD-TYPE  91 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      1    3
  ALPP WILD-TYPE   91  378
     clus
vv    ALPP MUTATED ALPP WILD-TYPE
  NO             1             91
  YES            3            378
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALPP MUTATED                                  1     0
  ALPP WILD-TYPE                                0     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALPP MUTATED                           0     3
  ALPP WILD-TYPE                        15   435
D132V7, multiclass
                                  clus
vv                                 ALPP MUTATED ALPP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V8, binary
                cls
clus               0   1
  ALPP MUTATED     1   1
  ALPP WILD-TYPE  17 419
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      1    1
  ALPP WILD-TYPE   17  419
                        clus
vv                       ALPP MUTATED ALPP WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            1            419
[1] 2 2
[1] FALSE

Clustering(133) Variable = CDH3 MUTATION ANALYSIS
D133V1, survival
                sevent
clus2              0   1
  CDH3 MUTATED     2   1
  CDH3 WILD-TYPE 376  92
  CDH3 MUTATED CDH3 WILD-TYPE 
             3            468 
  CDH3 MUTATED CDH3 WILD-TYPE 
             1             92 
$`CDH3 MUTATED`
TCGA-DU-6392 TCGA-FG-A711 TCGA-S9-A6U2 
      211.17        48.69        23.64 

$`CDH3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       36.66        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 
       34.49        31.33        28.70        22.95        17.62        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  CDH3 MUTATED CDH3 WILD-TYPE 
         23.64           0.03 
  CDH3 MUTATED CDH3 WILD-TYPE 
        211.17         182.33 
  CDH3 MUTATED CDH3 WILD-TYPE 
         48.69          18.56 
[1] "23.6 - 211.2 (48.7)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.2"
D133V2, continuous
D133V3, binary
                cls
clus               0   1
  CDH3 MUTATED     3   0
  CDH3 WILD-TYPE 204 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      3    0
  CDH3 WILD-TYPE  204  266
        clus
vv       CDH3 MUTATED CDH3 WILD-TYPE
  FEMALE            3            204
  MALE              0            266
[1] 2 2
[1] FALSE
D133V4, continuous
[1] "Remove cluster labels:" "CDH3 MUTATED"          
clus
  CDH3 MUTATED CDH3 WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66D 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DH-A7UV     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-7011     TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-7019     TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-7300     TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-7306     TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-8162     TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-8168     TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-A5TU     TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-A6S7     TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-A7T8     TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-DU-A7TD     TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-E1-5304     TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-E1-A7YV     TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-5965     TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-6691     TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-8185     TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-8189     TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-A60J     TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615     TCGA-HT-A617 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6TZ     TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U5 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA     TCGA-S9-A6UB 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG     TCGA-S9-A6WH 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM     TCGA-S9-A6WN 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A6WQ     TCGA-S9-A7IQ 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CDH3 MUTATED             1                0                 2
  CDH3 WILD-TYPE         174              119               177
D133V5, multiclass
                   clus
vv                  CDH3 MUTATED CDH3 WILD-TYPE
  ASTROCYTOMA                  1            174
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V6, binary
                cls
clus               0   1
  CDH3 MUTATED     1   2
  CDH3 WILD-TYPE  91 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      1    2
  CDH3 WILD-TYPE   91  379
     clus
vv    CDH3 MUTATED CDH3 WILD-TYPE
  NO             1             91
  YES            2            379
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH3 MUTATED                                  0     0
  CDH3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDH3 MUTATED                           0     3
  CDH3 WILD-TYPE                        15   435
D133V7, multiclass
                                  clus
vv                                 CDH3 MUTATED CDH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       3            435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V8, binary
                cls
clus               0   1
  CDH3 MUTATED     0   3
  CDH3 WILD-TYPE  18 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      0    3
  CDH3 WILD-TYPE   18  417
                        clus
vv                       CDH3 MUTATED CDH3 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            417
[1] 2 2
[1] FALSE

Clustering(134) Variable = NADSYN1 MUTATION ANALYSIS
D134V1, survival
                   sevent
clus2                 0   1
  NADSYN1 MUTATED     3   0
  NADSYN1 WILD-TYPE 375  93
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
                3               468 
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
                0                93 
$`NADSYN1 MUTATED`
TCGA-DU-6392 TCGA-FG-8188 TCGA-RY-A83Z 
      211.17        14.96         9.90 

$`NADSYN1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
             9.90              0.03 
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
           211.17            182.33 
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
            14.96             18.61 
[1] "9.9 - 211.2 (15.0)" "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D134V2, continuous
D134V3, binary
                   cls
clus                  0   1
  NADSYN1 MUTATED     2   1
  NADSYN1 WILD-TYPE 205 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NADSYN1 MUTATED      2    1
  NADSYN1 WILD-TYPE  205  265
        clus
vv       NADSYN1 MUTATED NADSYN1 WILD-TYPE
  FEMALE               2               205
  MALE                 1               265
[1] 2 2
[1] FALSE
D134V4, continuous
[1] "Remove cluster labels:" "NADSYN1 MUTATED"       
clus
  NADSYN1 MUTATED NADSYN1 WILD-TYPE 
                1               268 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YO 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6        TCGA-FG-5963 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8189 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A60J 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3        TCGA-FG-A711 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468        TCGA-HT-7470 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7485        TCGA-HT-7607 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689        TCGA-HT-7692 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7875 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R7 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-A618        TCGA-HT-A61A        TCGA-HT-A61B        TCGA-HT-A61C 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-HT-A74L        TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-P5-A731        TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-QH-A86X        TCGA-QH-A870        TCGA-RY-A83Y        TCGA-RY-A840 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-RY-A845        TCGA-RY-A847        TCGA-S9-A6TS        TCGA-S9-A6TU 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX        TCGA-S9-A6TY 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1        TCGA-S9-A6U2 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6U5        TCGA-S9-A6U6        TCGA-S9-A6U8        TCGA-S9-A6UA 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE        TCGA-S9-A6WG 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL        TCGA-S9-A6WM 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP        TCGA-S9-A6WQ 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX        TCGA-S9-A7IY 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1        TCGA-S9-A7J2 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX        TCGA-S9-A7QY 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R2        TCGA-S9-A7R3 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89V 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
       TCGA-VM-A8CE        TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" "NADSYN1 WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NADSYN1 MUTATED             2                1                 0
  NADSYN1 WILD-TYPE         173              118               179
D134V5, multiclass
                   clus
vv                  NADSYN1 MUTATED NADSYN1 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               0               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V6, binary
                   cls
clus                  0   1
  NADSYN1 MUTATED     1   2
  NADSYN1 WILD-TYPE  91 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NADSYN1 MUTATED      1    2
  NADSYN1 WILD-TYPE   91  379
     clus
vv    NADSYN1 MUTATED NADSYN1 WILD-TYPE
  NO                1                91
  YES               2               379
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NADSYN1 MUTATED                                  0     0
  NADSYN1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NADSYN1 MUTATED                           0     3
  NADSYN1 WILD-TYPE                        15   435
D134V7, multiclass
                                  clus
vv                                 NADSYN1 MUTATED NADSYN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V8, binary
                   cls
clus                  0   1
  NADSYN1 MUTATED     0   3
  NADSYN1 WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NADSYN1 MUTATED      0    3
  NADSYN1 WILD-TYPE   18  417
                        clus
vv                       NADSYN1 MUTATED NADSYN1 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               417
[1] 2 2
[1] FALSE

Clustering(135) Variable = LHFPL1 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  LHFPL1 MUTATED     3   1
  LHFPL1 WILD-TYPE 375  92
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
               4              467 
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
               1               92 
$`LHFPL1 MUTATED`
TCGA-FG-A6IZ TCGA-HT-7688 TCGA-IK-8125 TCGA-S9-A6TS 
       15.02        31.69        42.77        62.17 

$`LHFPL1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        19.00        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
           15.02             0.03 
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
           62.17           211.17 
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
           37.23            18.61 
[1] "15.0 - 62.2 (37.2)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1"  
D135V2, continuous
D135V3, binary
                  cls
clus                 0   1
  LHFPL1 MUTATED     1   3
  LHFPL1 WILD-TYPE 206 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LHFPL1 MUTATED      1    3
  LHFPL1 WILD-TYPE  206  263
        clus
vv       LHFPL1 MUTATED LHFPL1 WILD-TYPE
  FEMALE              1              206
  MALE                3              263
[1] 2 2
[1] FALSE
D135V4, continuous
[1] "Remove cluster labels:" "LHFPL1 MUTATED"        
clus
  LHFPL1 MUTATED LHFPL1 WILD-TYPE 
               1              268 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DB-A75L       TCGA-DB-A75O       TCGA-DH-5140       TCGA-DH-5142 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B       TCGA-DH-A66D 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DH-A66G       TCGA-DH-A7UR       TCGA-DH-A7UU 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DH-A7UV       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-7011       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-DU-A6S2       TCGA-DU-A6S6 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-A6S7       TCGA-DU-A6S8       TCGA-DU-A76R       TCGA-DU-A7T6 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-A7T8       TCGA-DU-A7TA       TCGA-DU-A7TB       TCGA-DU-A7TC 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-DU-A7TD       TCGA-DU-A7TG       TCGA-E1-5302       TCGA-E1-5303 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-E1-A7YO 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-E1-A7YV       TCGA-E1-A7YW       TCGA-E1-A7Z6       TCGA-FG-5963 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-FG-A60L       TCGA-FG-A6J1       TCGA-FG-A6J3 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-FG-A711       TCGA-FG-A713       TCGA-FG-A87Q       TCGA-HT-7468 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-HT-A61B 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-HT-A61C       TCGA-HT-A74L       TCGA-IK-7675       TCGA-KT-A74X 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-KT-A7W1       TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-P5-A5EX       TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-P5-A5F6       TCGA-P5-A731       TCGA-QH-A65R       TCGA-QH-A65S 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-QH-A65V       TCGA-QH-A65X       TCGA-QH-A65Z       TCGA-QH-A6CS 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-QH-A6CU       TCGA-QH-A6CV       TCGA-QH-A6CW       TCGA-QH-A6CX 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-QH-A6CY       TCGA-QH-A6CZ       TCGA-QH-A6X3       TCGA-QH-A6X4 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-QH-A6X5       TCGA-QH-A6X8       TCGA-QH-A6X9       TCGA-QH-A6XA 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-QH-A6XC       TCGA-QH-A86X       TCGA-QH-A870       TCGA-RY-A83Y 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-RY-A840       TCGA-RY-A845       TCGA-RY-A847       TCGA-S9-A6TU 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6TV       TCGA-S9-A6TW       TCGA-S9-A6TX       TCGA-S9-A6TY 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6TZ       TCGA-S9-A6U0       TCGA-S9-A6U1       TCGA-S9-A6U2 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6U5       TCGA-S9-A6U6       TCGA-S9-A6U8       TCGA-S9-A6UA 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6UB       TCGA-S9-A6WD       TCGA-S9-A6WE       TCGA-S9-A6WG 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6WH       TCGA-S9-A6WI       TCGA-S9-A6WL       TCGA-S9-A6WM 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A6WN       TCGA-S9-A6WO       TCGA-S9-A6WP       TCGA-S9-A6WQ 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A7IQ       TCGA-S9-A7IS       TCGA-S9-A7IX       TCGA-S9-A7IY 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A7IZ       TCGA-S9-A7J0       TCGA-S9-A7J1       TCGA-S9-A7J2 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A7J3       TCGA-S9-A7QW       TCGA-S9-A7QX       TCGA-S9-A7QY 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A7QZ       TCGA-S9-A7R1       TCGA-S9-A7R2       TCGA-S9-A7R3 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A7R4       TCGA-S9-A7R7       TCGA-S9-A7R8       TCGA-S9-A89V 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-S9-A89Z       TCGA-TM-A7C3       TCGA-TM-A7C4       TCGA-TM-A7C5 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-TM-A7CA       TCGA-TM-A7CF       TCGA-TM-A84B       TCGA-TM-A84C 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-TM-A84F       TCGA-TM-A84G       TCGA-TM-A84H       TCGA-TM-A84I 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-TM-A84J       TCGA-TM-A84L       TCGA-TM-A84M       TCGA-TM-A84O 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-TM-A84Q       TCGA-TM-A84R       TCGA-TM-A84S       TCGA-TM-A84T 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-TQ-A7RW       TCGA-VM-A8C8       TCGA-VM-A8CA       TCGA-VM-A8CD 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
      TCGA-VM-A8CE       TCGA-VM-A8CH       TCGA-WY-A858       TCGA-WY-A859 
"LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" "LHFPL1 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  LHFPL1 MUTATED             1                1                 2
  LHFPL1 WILD-TYPE         174              118               177
D135V5, multiclass
                   clus
vv                  LHFPL1 MUTATED LHFPL1 WILD-TYPE
  ASTROCYTOMA                    1              174
  OLIGOASTROCYTOMA               1              118
  OLIGODENDROGLIOMA              2              177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V6, binary
                  cls
clus                 0   1
  LHFPL1 MUTATED     1   3
  LHFPL1 WILD-TYPE  91 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LHFPL1 MUTATED      1    3
  LHFPL1 WILD-TYPE   91  378
     clus
vv    LHFPL1 MUTATED LHFPL1 WILD-TYPE
  NO               1               91
  YES              3              378
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LHFPL1 MUTATED                                  0     0
  LHFPL1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LHFPL1 MUTATED                           0     4
  LHFPL1 WILD-TYPE                        15   434
D135V7, multiclass
                                  clus
vv                                 LHFPL1 MUTATED LHFPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                8
  BLACK OR AFRICAN AMERICAN                     0               15
  WHITE                                         4              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V8, binary
                  cls
clus                 0   1
  LHFPL1 MUTATED     0   4
  LHFPL1 WILD-TYPE  18 416
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LHFPL1 MUTATED      0    4
  LHFPL1 WILD-TYPE   18  416
                        clus
vv                       LHFPL1 MUTATED LHFPL1 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              416
[1] 2 2
[1] FALSE

Clustering(136) Variable = CXCR2 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  CXCR2 MUTATED     4   0
  CXCR2 WILD-TYPE 374  93
  CXCR2 MUTATED CXCR2 WILD-TYPE 
              4             467 
  CXCR2 MUTATED CXCR2 WILD-TYPE 
              0              93 
$`CXCR2 MUTATED`
TCGA-CS-6670 TCGA-DU-7309 TCGA-HT-7478 TCGA-P5-A5EZ 
        6.61         2.76         6.38         2.30 

$`CXCR2 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54        24.26        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  CXCR2 MUTATED CXCR2 WILD-TYPE 
           2.30            0.03 
  CXCR2 MUTATED CXCR2 WILD-TYPE 
           6.61          211.17 
  CXCR2 MUTATED CXCR2 WILD-TYPE 
           4.57           18.71 
[1] "2.3 - 6.6 (4.6)"    "0.0 - 211.2 (18.7)"
[1] "hr="    "450000"
D136V2, continuous
D136V3, binary
                 cls
clus                0   1
  CXCR2 MUTATED     1   3
  CXCR2 WILD-TYPE 206 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR2 MUTATED      1    3
  CXCR2 WILD-TYPE  206  263
        clus
vv       CXCR2 MUTATED CXCR2 WILD-TYPE
  FEMALE             1             206
  MALE               3             263
[1] 2 2
[1] FALSE
D136V4, continuous
[1] "Remove cluster labels:" "CXCR2 MUTATED"         
clus
  CXCR2 MUTATED CXCR2 WILD-TYPE 
              1             268 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DB-A75L      TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DH-5143      TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DH-A66F      TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DH-A7UV      TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-7011      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-A60L      TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-FG-A713      TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-7475      TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-7609      TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-7693      TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-7884      TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-A5RA      TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-A618      TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-HT-A74L      TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-P5-A731      TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-QH-A65X      TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-QH-A6CV      TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-QH-A6CZ      TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-QH-A6X8      TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-QH-A86X      TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-RY-A845      TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6TV      TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6TZ      TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6U5      TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6UB      TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6WH      TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A6WN      TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A7IQ      TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A7IZ      TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A7J3      TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A7QZ      TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A7R4      TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-S9-A89Z      TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-TM-A7CA      TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-TM-A84F      TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-TM-A84J      TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-TM-A84Q      TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-TQ-A7RW      TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
     TCGA-VM-A8CE      TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" "CXCR2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CXCR2 MUTATED             2                0                 2
  CXCR2 WILD-TYPE         173              119               177
D136V5, multiclass
                   clus
vv                  CXCR2 MUTATED CXCR2 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             2             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V6, binary
                 cls
clus                0   1
  CXCR2 MUTATED     2   2
  CXCR2 WILD-TYPE  90 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR2 MUTATED      2    2
  CXCR2 WILD-TYPE   90  379
     clus
vv    CXCR2 MUTATED CXCR2 WILD-TYPE
  NO              2              90
  YES             2             379
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXCR2 MUTATED                                  0     0
  CXCR2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXCR2 MUTATED                           0     4
  CXCR2 WILD-TYPE                        15   434
D136V7, multiclass
                                  clus
vv                                 CXCR2 MUTATED CXCR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V8, binary
                 cls
clus                0   1
  CXCR2 MUTATED     0   4
  CXCR2 WILD-TYPE  18 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR2 MUTATED      0    4
  CXCR2 WILD-TYPE   18  416
                        clus
vv                       CXCR2 MUTATED CXCR2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             416
[1] 2 2
[1] FALSE

Clustering(137) Variable = SEC14L4 MUTATION ANALYSIS
D137V1, survival
                   sevent
clus2                 0   1
  SEC14L4 MUTATED     2   1
  SEC14L4 WILD-TYPE 376  92
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
                3               468 
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
                1                92 
$`SEC14L4 MUTATED`
TCGA-HT-7469 TCGA-HT-7858 TCGA-TM-A84I 
       11.54        50.63        28.08 

$`SEC14L4 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
            11.54              0.03 
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
            50.63            211.17 
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
            28.08             18.61 
[1] "11.5 - 50.6 (28.1)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.6"
D137V2, continuous
D137V3, binary
                   cls
clus                  0   1
  SEC14L4 MUTATED     0   3
  SEC14L4 WILD-TYPE 207 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L4 MUTATED      0    3
  SEC14L4 WILD-TYPE  207  263
        clus
vv       SEC14L4 MUTATED SEC14L4 WILD-TYPE
  FEMALE               0               207
  MALE                 3               263
[1] 2 2
[1] FALSE
D137V4, continuous
[1] "Remove cluster labels:" "SEC14L4 MUTATED"       
clus
  SEC14L4 MUTATED SEC14L4 WILD-TYPE 
                1               268 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T6 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TA        TCGA-DU-A7TB        TCGA-DU-A7TC 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-DU-A7TD        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-E1-A7YO 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-E1-A7YV        TCGA-E1-A7YW        TCGA-E1-A7Z6        TCGA-FG-5963 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7485 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A61A        TCGA-HT-A61B 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-HT-A61C        TCGA-HT-A74L        TCGA-IK-7675        TCGA-KT-A74X 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-KT-A7W1        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F4 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-P5-A5F6        TCGA-P5-A731        TCGA-QH-A65R        TCGA-QH-A65S 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-QH-A65V        TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-QH-A6CU        TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870        TCGA-RY-A83Y 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-RY-A840        TCGA-RY-A845        TCGA-RY-A847        TCGA-S9-A6TS 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6        TCGA-S9-A6U8 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R1        TCGA-S9-A7R2 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-S9-A89V        TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-TM-A7C5        TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-TM-A84C        TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-TQ-A7RW        TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
       TCGA-VM-A8CE        TCGA-VM-A8CH        TCGA-WY-A858        TCGA-WY-A859 
"SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" "SEC14L4 WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SEC14L4 MUTATED             2                0                 1
  SEC14L4 WILD-TYPE         173              119               178
D137V5, multiclass
                   clus
vv                  SEC14L4 MUTATED SEC14L4 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                0               119
  OLIGODENDROGLIOMA               1               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V6, binary
                   cls
clus                  0   1
  SEC14L4 MUTATED     2   1
  SEC14L4 WILD-TYPE  90 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L4 MUTATED      2    1
  SEC14L4 WILD-TYPE   90  380
     clus
vv    SEC14L4 MUTATED SEC14L4 WILD-TYPE
  NO                2                90
  YES               1               380
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC14L4 MUTATED                                  0     0
  SEC14L4 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SEC14L4 MUTATED                           0     3
  SEC14L4 WILD-TYPE                        15   435
D137V7, multiclass
                                  clus
vv                                 SEC14L4 MUTATED SEC14L4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V8, binary
                   cls
clus                  0   1
  SEC14L4 MUTATED     0   3
  SEC14L4 WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L4 MUTATED      0    3
  SEC14L4 WILD-TYPE   18  417
                        clus
vv                       SEC14L4 MUTATED SEC14L4 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               417
[1] 2 2
[1] FALSE

Clustering(138) Variable = ANKRD17 MUTATION ANALYSIS
D138V1, survival
                   sevent
clus2                 0   1
  ANKRD17 MUTATED     6   0
  ANKRD17 WILD-TYPE 372  93
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                6               465 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                0                93 
$`ANKRD17 MUTATED`
TCGA-DU-6392 TCGA-DU-A5TW TCGA-HT-7687 TCGA-HT-7694 TCGA-QH-A6CY TCGA-S9-A6TX 
      211.17         5.65         0.10         6.90         2.20        34.49 

$`ANKRD17 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61        12.23         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        18.77        37.84        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
             0.10              0.03 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
           211.17            182.33 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
            6.275            18.610 
[1] "0.1 - 211.2 (6.3)"  "0.0 - 182.3 (18.6)"
[1] "hr="   "1e+07"
D138V2, continuous
D138V3, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED     2   4
  ANKRD17 WILD-TYPE 205 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED      2    4
  ANKRD17 WILD-TYPE  205  262
        clus
vv       ANKRD17 MUTATED ANKRD17 WILD-TYPE
  FEMALE               2               205
  MALE                 4               262
[1] 2 2
[1] FALSE
D138V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ANKRD17 MUTATED             2                1                 3
  ANKRD17 WILD-TYPE         173              118               176
D138V5, multiclass
                   clus
vv                  ANKRD17 MUTATED ANKRD17 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                1               118
  OLIGODENDROGLIOMA               3               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V6, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED     2   4
  ANKRD17 WILD-TYPE  90 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED      2    4
  ANKRD17 WILD-TYPE   90  377
     clus
vv    ANKRD17 MUTATED ANKRD17 WILD-TYPE
  NO                2                90
  YES               4               377
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD17 MUTATED                                  0     0
  ANKRD17 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD17 MUTATED                           1     5
  ANKRD17 WILD-TYPE                        14   433
D138V7, multiclass
                                  clus
vv                                 ANKRD17 MUTATED ANKRD17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          5               433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V8, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED     0   6
  ANKRD17 WILD-TYPE  18 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED      0    6
  ANKRD17 WILD-TYPE   18  414
                        clus
vv                       ANKRD17 MUTATED ANKRD17 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               6               414
[1] 2 2
[1] FALSE

Clustering(139) Variable = MAST3 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2               0   1
  MAST3 MUTATED     5   0
  MAST3 WILD-TYPE 373  93
  MAST3 MUTATED MAST3 WILD-TYPE 
              5             466 
  MAST3 MUTATED MAST3 WILD-TYPE 
              0              93 
$`MAST3 MUTATED`
TCGA-DU-A6S2 TCGA-FG-A6IZ TCGA-HT-7856 TCGA-HT-7884 TCGA-KT-A7W1 
        8.65        15.02        39.09        11.28        14.40 

$`MAST3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65         5.65        12.20         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        18.44        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        19.23         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  MAST3 MUTATED MAST3 WILD-TYPE 
           8.65            0.03 
  MAST3 MUTATED MAST3 WILD-TYPE 
          39.09          211.17 
  MAST3 MUTATED MAST3 WILD-TYPE 
          14.40           18.66 
[1] "8.7 - 39.1 (14.4)"  "0.0 - 211.2 (18.7)"
[1] "hr="     "3300000"
D139V2, continuous
D139V3, binary
                 cls
clus                0   1
  MAST3 MUTATED     3   2
  MAST3 WILD-TYPE 204 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAST3 MUTATED      3    2
  MAST3 WILD-TYPE  204  264
        clus
vv       MAST3 MUTATED MAST3 WILD-TYPE
  FEMALE             3             204
  MALE               2             264
[1] 2 2
[1] FALSE
D139V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  MAST3 MUTATED             2                0                 3
  MAST3 WILD-TYPE         173              119               176
D139V5, multiclass
                   clus
vv                  MAST3 MUTATED MAST3 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             3             176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V6, binary
                 cls
clus                0   1
  MAST3 MUTATED     1   4
  MAST3 WILD-TYPE  91 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAST3 MUTATED      1    4
  MAST3 WILD-TYPE   91  377
     clus
vv    MAST3 MUTATED MAST3 WILD-TYPE
  NO              1              91
  YES             4             377
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAST3 MUTATED                                  0     0
  MAST3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAST3 MUTATED                           1     4
  MAST3 WILD-TYPE                        14   434
D139V7, multiclass
                                  clus
vv                                 MAST3 MUTATED MAST3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    1              14
  WHITE                                        4             434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V8, binary
                 cls
clus                0   1
  MAST3 MUTATED     0   5
  MAST3 WILD-TYPE  18 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAST3 MUTATED      0    5
  MAST3 WILD-TYPE   18  415
                        clus
vv                       MAST3 MUTATED MAST3 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             415
[1] 2 2
[1] FALSE

Clustering(140) Variable = AMMECR1 MUTATION ANALYSIS
D140V1, survival
                   sevent
clus2                 0   1
  AMMECR1 MUTATED     3   0
  AMMECR1 WILD-TYPE 375  93
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               468 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                0                93 
$`AMMECR1 MUTATED`
TCGA-CS-6665 TCGA-DH-5144 TCGA-HT-A61B 
       12.43         8.02        17.52 

$`AMMECR1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        18.44        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.74        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A 
       16.93         1.81        16.14        16.83        21.40         6.38 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
             8.02              0.03 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            17.52            211.17 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            12.43             18.66 
[1] "8.0 - 17.5 (12.4)"  "0.0 - 211.2 (18.7)"
[1] "hr="     "1200000"
D140V2, continuous
D140V3, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     2   1
  AMMECR1 WILD-TYPE 205 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      2    1
  AMMECR1 WILD-TYPE  205  265
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  FEMALE               2               205
  MALE                 1               265
[1] 2 2
[1] FALSE
D140V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMMECR1 MUTATED             2                0                 1
  AMMECR1 WILD-TYPE         173              119               178
D140V5, multiclass
                   clus
vv                  AMMECR1 MUTATED AMMECR1 WILD-TYPE
  ASTROCYTOMA                     2               173
  OLIGOASTROCYTOMA                0               119
  OLIGODENDROGLIOMA               1               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V6, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     2   1
  AMMECR1 WILD-TYPE  90 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      2    1
  AMMECR1 WILD-TYPE   90  380
     clus
vv    AMMECR1 MUTATED AMMECR1 WILD-TYPE
  NO                2                90
  YES               1               380
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMMECR1 MUTATED                                  0     0
  AMMECR1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AMMECR1 MUTATED                           0     3
  AMMECR1 WILD-TYPE                        15   435
D140V7, multiclass
                                  clus
vv                                 AMMECR1 MUTATED AMMECR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 8
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          3               435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V8, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     0   3
  AMMECR1 WILD-TYPE  18 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      0    3
  AMMECR1 WILD-TYPE   18  417
                        clus
vv                       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               3               417
[1] 2 2
[1] FALSE

Clustering(141) Variable = NEO1 MUTATION ANALYSIS
D141V1, survival
                sevent
clus2              0   1
  NEO1 MUTATED     7   0
  NEO1 WILD-TYPE 371  93
  NEO1 MUTATED NEO1 WILD-TYPE 
             7            464 
  NEO1 MUTATED NEO1 WILD-TYPE 
             0             93 
$`NEO1 MUTATED`
TCGA-DB-5270 TCGA-DH-A66D TCGA-DU-6392 TCGA-HT-7687 TCGA-IK-8125 TCGA-RY-A83X 
      122.73        27.81       211.17         0.10        42.77        30.87 
TCGA-S9-A6WQ 
       14.07 

$`NEO1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
       78.21        95.57       130.78        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       18.44        15.35        17.88        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
       16.24         0.76        44.68         6.05        42.74        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C 
       16.14        16.83        21.40         6.38        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       19.89         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        59.38         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  NEO1 MUTATED NEO1 WILD-TYPE 
          0.10           0.03 
  NEO1 MUTATED NEO1 WILD-TYPE 
        211.17         182.33 
  NEO1 MUTATED NEO1 WILD-TYPE 
         30.87          18.56 
[1] "0.1 - 211.2 (30.9)" "0.0 - 182.3 (18.6)"
[1] "hr="     "2.7e+07"
D141V2, continuous
D141V3, binary
                cls
clus               0   1
  NEO1 MUTATED     5   2
  NEO1 WILD-TYPE 202 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEO1 MUTATED      5    2
  NEO1 WILD-TYPE  202  264
        clus
vv       NEO1 MUTATED NEO1 WILD-TYPE
  FEMALE            5            202
  MALE              2            264
[1] 2 2
[1] FALSE
D141V4, continuous
[1] "Remove cluster labels:" "NEO1 MUTATED"          
clus
  NEO1 MUTATED NEO1 WILD-TYPE 
             2            267 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DB-A75L     TCGA-DB-A75O     TCGA-DH-5140     TCGA-DH-5142 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DH-5143     TCGA-DH-5144     TCGA-DH-A66B     TCGA-DH-A66F 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DH-A66G     TCGA-DH-A7UR     TCGA-DH-A7UU     TCGA-DH-A7UV 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853     TCGA-DU-5854 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871     TCGA-DU-5874 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404     TCGA-DU-6405 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410     TCGA-DU-7011 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018     TCGA-DU-7019 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299     TCGA-DU-7300 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304     TCGA-DU-7306 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161     TCGA-DU-8162 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167     TCGA-DU-8168 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS     TCGA-DU-A5TU 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-A5TW     TCGA-DU-A6S2     TCGA-DU-A6S6     TCGA-DU-A6S7 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-A6S8     TCGA-DU-A76R     TCGA-DU-A7T6     TCGA-DU-A7T8 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-A7TA     TCGA-DU-A7TB     TCGA-DU-A7TC     TCGA-DU-A7TD 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-DU-A7TG     TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311     TCGA-E1-5318 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-E1-5319     TCGA-E1-5322     TCGA-E1-A7YO     TCGA-E1-A7YV 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-E1-A7YW     TCGA-E1-A7Z6     TCGA-FG-5963     TCGA-FG-5965 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-6688     TCGA-FG-6689     TCGA-FG-6690     TCGA-FG-6691 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-7636     TCGA-FG-7638     TCGA-FG-8181     TCGA-FG-8185 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-8186     TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-A4MT     TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-A60L     TCGA-FG-A6J1     TCGA-FG-A6J3     TCGA-FG-A711 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-FG-A713     TCGA-FG-A87Q     TCGA-HT-7468     TCGA-HT-7470 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485     TCGA-HT-7607 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689     TCGA-HT-7692 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854     TCGA-HT-7875 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV     TCGA-HT-A5R7 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615     TCGA-HT-A617 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-A618     TCGA-HT-A61A     TCGA-HT-A61B     TCGA-HT-A61C 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-HT-A74L     TCGA-IK-7675     TCGA-KT-A74X     TCGA-KT-A7W1 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-P5-A731     TCGA-QH-A65R     TCGA-QH-A65S     TCGA-QH-A65V 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-QH-A65X     TCGA-QH-A65Z     TCGA-QH-A6CS     TCGA-QH-A6CU 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-QH-A6CV     TCGA-QH-A6CW     TCGA-QH-A6CX     TCGA-QH-A6CY 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-QH-A6CZ     TCGA-QH-A6X3     TCGA-QH-A6X4     TCGA-QH-A6X5 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-QH-A6X8     TCGA-QH-A6X9     TCGA-QH-A6XA     TCGA-QH-A6XC 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-QH-A86X     TCGA-QH-A870     TCGA-RY-A83Y     TCGA-RY-A840 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-RY-A845     TCGA-RY-A847     TCGA-S9-A6TS     TCGA-S9-A6TU 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6TV     TCGA-S9-A6TW     TCGA-S9-A6TX     TCGA-S9-A6TY 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6TZ     TCGA-S9-A6U0     TCGA-S9-A6U1     TCGA-S9-A6U2 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6U5     TCGA-S9-A6U6     TCGA-S9-A6U8     TCGA-S9-A6UA 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6UB     TCGA-S9-A6WD     TCGA-S9-A6WE     TCGA-S9-A6WG 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6WH     TCGA-S9-A6WI     TCGA-S9-A6WL     TCGA-S9-A6WM 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A6WN     TCGA-S9-A6WO     TCGA-S9-A6WP     TCGA-S9-A7IQ 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A7IS     TCGA-S9-A7IX     TCGA-S9-A7IY     TCGA-S9-A7IZ 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A7J0     TCGA-S9-A7J1     TCGA-S9-A7J2     TCGA-S9-A7J3 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A7QW     TCGA-S9-A7QX     TCGA-S9-A7QY     TCGA-S9-A7QZ 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A7R1     TCGA-S9-A7R2     TCGA-S9-A7R3     TCGA-S9-A7R4 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-S9-A7R7     TCGA-S9-A7R8     TCGA-S9-A89V     TCGA-S9-A89Z 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-TM-A7C3     TCGA-TM-A7C4     TCGA-TM-A7C5     TCGA-TM-A7CA 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-TM-A7CF     TCGA-TM-A84B     TCGA-TM-A84C     TCGA-TM-A84F 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-TM-A84G     TCGA-TM-A84H     TCGA-TM-A84I     TCGA-TM-A84J 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-TM-A84L     TCGA-TM-A84M     TCGA-TM-A84O     TCGA-TM-A84Q 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-TM-A84R     TCGA-TM-A84S     TCGA-TM-A84T     TCGA-TQ-A7RW 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-VM-A8C8     TCGA-VM-A8CA     TCGA-VM-A8CD     TCGA-VM-A8CE 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
    TCGA-VM-A8CH     TCGA-WY-A858     TCGA-WY-A859 
"NEO1 WILD-TYPE" "NEO1 WILD-TYPE" "NEO1 WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NEO1 MUTATED             2                3                 2
  NEO1 WILD-TYPE         173              116               177
D141V5, multiclass
                   clus
vv                  NEO1 MUTATED NEO1 WILD-TYPE
  ASTROCYTOMA                  2            173
  OLIGOASTROCYTOMA             3            116
  OLIGODENDROGLIOMA            2            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V6, binary
                cls
clus               0   1
  NEO1 MUTATED     1   6
  NEO1 WILD-TYPE  91 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEO1 MUTATED      1    6
  NEO1 WILD-TYPE   91  375
     clus
vv    NEO1 MUTATED NEO1 WILD-TYPE
  NO             1             91
  YES            6            375
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEO1 MUTATED                                  0     0
  NEO1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEO1 MUTATED                           0     7
  NEO1 WILD-TYPE                        15   431
D141V7, multiclass
                                  clus
vv                                 NEO1 MUTATED NEO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       7            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V8, binary
                cls
clus               0   1
  NEO1 MUTATED     0   7
  NEO1 WILD-TYPE  18 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEO1 MUTATED      0    7
  NEO1 WILD-TYPE   18  413
                        clus
vv                       NEO1 MUTATED NEO1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            7            413
[1] 2 2
[1] FALSE

Clustering(142) Variable = IGSF8 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2               0   1
  IGSF8 MUTATED     3   0
  IGSF8 WILD-TYPE 375  93
  IGSF8 MUTATED IGSF8 WILD-TYPE 
              3             468 
  IGSF8 MUTATED IGSF8 WILD-TYPE 
              0              93 
$`IGSF8 MUTATED`
TCGA-DB-A64L TCGA-DU-6392 TCGA-FG-7636 
       24.20       211.17        17.88 

$`IGSF8 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        0.56        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        40.08        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
        5.56        13.78         0.23        29.59        34.19        13.74 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B 
        1.81        16.14        16.83        21.40         6.38        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  IGSF8 MUTATED IGSF8 WILD-TYPE 
          17.88            0.03 
  IGSF8 MUTATED IGSF8 WILD-TYPE 
         211.17          182.33 
  IGSF8 MUTATED IGSF8 WILD-TYPE 
          24.20           18.61 
[1] "17.9 - 211.2 (24.2)" "0.0 - 182.3 (18.6)" 
[1] "hr="   "1e+07"
D142V2, continuous
D142V3, binary
                 cls
clus                0   1
  IGSF8 MUTATED     2   1
  IGSF8 WILD-TYPE 205 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF8 MUTATED      2    1
  IGSF8 WILD-TYPE  205  265
        clus
vv       IGSF8 MUTATED IGSF8 WILD-TYPE
  FEMALE             2             205
  MALE               1             265
[1] 2 2
[1] FALSE
D142V4, continuous
[1] "Remove cluster labels:" "IGSF8 MUTATED"         
clus
  IGSF8 MUTATED IGSF8 WILD-TYPE 
              2             267 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S      TCGA-DB-A64U 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X      TCGA-DB-A75L 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DB-A75O      TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DH-5144      TCGA-DH-A66B      TCGA-DH-A66D      TCGA-DH-A66F 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DH-A66G      TCGA-DH-A7UR      TCGA-DH-A7UU      TCGA-DH-A7UV 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-5851      TCGA-DU-5852      TCGA-DU-5853      TCGA-DU-5854 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-5855      TCGA-DU-5870      TCGA-DU-5871      TCGA-DU-5874 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-6396      TCGA-DU-6403      TCGA-DU-6404      TCGA-DU-6405 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-6407      TCGA-DU-6408      TCGA-DU-6410      TCGA-DU-7011 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018      TCGA-DU-7019 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299      TCGA-DU-7300 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304      TCGA-DU-7306 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161      TCGA-DU-8162 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167      TCGA-DU-8168 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS      TCGA-DU-A5TU 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-A5TW      TCGA-DU-A6S2      TCGA-DU-A6S6      TCGA-DU-A6S7 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-A6S8      TCGA-DU-A76R      TCGA-DU-A7T6      TCGA-DU-A7T8 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-A7TA      TCGA-DU-A7TB      TCGA-DU-A7TC      TCGA-DU-A7TD 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-DU-A7TG      TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311      TCGA-E1-5318 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-E1-5319      TCGA-E1-5322      TCGA-E1-A7YO      TCGA-E1-A7YV 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-E1-A7YW      TCGA-E1-A7Z6      TCGA-FG-5963      TCGA-FG-5965 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690      TCGA-FG-6691 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-7638      TCGA-FG-8181      TCGA-FG-8185      TCGA-FG-8186 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-8187      TCGA-FG-8188      TCGA-FG-8189      TCGA-FG-A4MT 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-A4MW      TCGA-FG-A4MX      TCGA-FG-A60J      TCGA-FG-A60L 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-A6J1      TCGA-FG-A6J3      TCGA-FG-A711      TCGA-FG-A713 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-FG-A87Q      TCGA-HT-7468      TCGA-HT-7470      TCGA-HT-7475 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607      TCGA-HT-7609 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692      TCGA-HT-7693 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875      TCGA-HT-7884 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7      TCGA-HT-A5RA 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-HT-A61A      TCGA-HT-A61B      TCGA-HT-A61C      TCGA-HT-A74L 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-IK-7675      TCGA-KT-A74X      TCGA-KT-A7W1      TCGA-P5-A5EU 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-P5-A5EV      TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-P5-A5F2      TCGA-P5-A5F4      TCGA-P5-A5F6      TCGA-P5-A731 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A65R      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65X 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A65Z      TCGA-QH-A6CS      TCGA-QH-A6CU      TCGA-QH-A6CV 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A6CW      TCGA-QH-A6CX      TCGA-QH-A6CY      TCGA-QH-A6CZ 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A6X3      TCGA-QH-A6X4      TCGA-QH-A6X5      TCGA-QH-A6X8 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A6X9      TCGA-QH-A6XA      TCGA-QH-A6XC      TCGA-QH-A86X 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-QH-A870      TCGA-RY-A83Y      TCGA-RY-A840      TCGA-RY-A845 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-RY-A847      TCGA-S9-A6TS      TCGA-S9-A6TU      TCGA-S9-A6TV 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6TW      TCGA-S9-A6TX      TCGA-S9-A6TY      TCGA-S9-A6TZ 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6U0      TCGA-S9-A6U1      TCGA-S9-A6U2      TCGA-S9-A6U5 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6U6      TCGA-S9-A6U8      TCGA-S9-A6UA      TCGA-S9-A6UB 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6WD      TCGA-S9-A6WE      TCGA-S9-A6WG      TCGA-S9-A6WH 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6WI      TCGA-S9-A6WL      TCGA-S9-A6WM      TCGA-S9-A6WN 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A6WO      TCGA-S9-A6WP      TCGA-S9-A6WQ      TCGA-S9-A7IQ 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A7IS      TCGA-S9-A7IX      TCGA-S9-A7IY      TCGA-S9-A7IZ 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A7J0      TCGA-S9-A7J1      TCGA-S9-A7J2      TCGA-S9-A7J3 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A7QW      TCGA-S9-A7QX      TCGA-S9-A7QY      TCGA-S9-A7QZ 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A7R1      TCGA-S9-A7R2      TCGA-S9-A7R3      TCGA-S9-A7R4 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-S9-A7R7      TCGA-S9-A7R8      TCGA-S9-A89V      TCGA-S9-A89Z 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-TM-A7C3      TCGA-TM-A7C4      TCGA-TM-A7C5      TCGA-TM-A7CA 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-TM-A7CF      TCGA-TM-A84B      TCGA-TM-A84C      TCGA-TM-A84F 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-TM-A84G      TCGA-TM-A84H      TCGA-TM-A84I      TCGA-TM-A84J 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-TM-A84L      TCGA-TM-A84M      TCGA-TM-A84O      TCGA-TM-A84Q 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-TM-A84R      TCGA-TM-A84S      TCGA-TM-A84T      TCGA-TQ-A7RW 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-VM-A8C8      TCGA-VM-A8CA      TCGA-VM-A8CD      TCGA-VM-A8CE 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
     TCGA-VM-A8CH      TCGA-WY-A858      TCGA-WY-A859 
"IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" "IGSF8 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IGSF8 MUTATED             2                0                 1
  IGSF8 WILD-TYPE         173              119               178
D142V5, multiclass
                   clus
vv                  IGSF8 MUTATED IGSF8 WILD-TYPE
  ASTROCYTOMA                   2             173
  OLIGOASTROCYTOMA              0             119
  OLIGODENDROGLIOMA             1             178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V6, binary
                 cls
clus                0   1
  IGSF8 MUTATED     2   1
  IGSF8 WILD-TYPE  90 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF8 MUTATED      2    1
  IGSF8 WILD-TYPE   90  380
     clus
vv    IGSF8 MUTATED IGSF8 WILD-TYPE
  NO              2              90
  YES             1             380
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGSF8 MUTATED                                  0     0
  IGSF8 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGSF8 MUTATED                           0     3
  IGSF8 WILD-TYPE                        15   435
D142V7, multiclass
                                  clus
vv                                 IGSF8 MUTATED IGSF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               8
  BLACK OR AFRICAN AMERICAN                    0              15
  WHITE                                        3             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V8, binary
                 cls
clus                0   1
  IGSF8 MUTATED     0   3
  IGSF8 WILD-TYPE  18 417
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF8 MUTATED      0    3
  IGSF8 WILD-TYPE   18  417
                        clus
vv                       IGSF8 MUTATED IGSF8 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             417
[1] 2 2
[1] FALSE

Clustering(143) Variable = RGS3 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  RGS3 MUTATED     4   1
  RGS3 WILD-TYPE 374  92
  RGS3 MUTATED RGS3 WILD-TYPE 
             5            466 
  RGS3 MUTATED RGS3 WILD-TYPE 
             1             92 
$`RGS3 MUTATED`
TCGA-DB-A75L TCGA-DH-A66B TCGA-DU-6392 TCGA-E1-5307 TCGA-HT-8564 
       11.24        42.05       211.17        57.93        15.72 

$`RGS3 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        12.10        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        30.21        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        41.13        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
       13.78         0.23        29.59        34.19        13.74        28.27 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61A TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.83        21.40         6.38        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        0.76         1.28         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  RGS3 MUTATED RGS3 WILD-TYPE 
         11.24           0.03 
  RGS3 MUTATED RGS3 WILD-TYPE 
        211.17         182.33 
  RGS3 MUTATED RGS3 WILD-TYPE 
         42.05          18.61 
[1] "11.2 - 211.2 (42.0)" "0.0 - 182.3 (18.6)" 
[1] "hr=" "2.6"
D143V2, continuous
D143V3, binary
                cls
clus               0   1
  RGS3 MUTATED     3   2
  RGS3 WILD-TYPE 204 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      3    2
  RGS3 WILD-TYPE  204  264
        clus
vv       RGS3 MUTATED RGS3 WILD-TYPE
  FEMALE            3            204
  MALE              2            264
[1] 2 2
[1] FALSE
D143V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  RGS3 MUTATED             5                0                 0
  RGS3 WILD-TYPE         170              119               179
D143V5, multiclass
                   clus
vv                  RGS3 MUTATED RGS3 WILD-TYPE
  ASTROCYTOMA                  5            170
  OLIGOASTROCYTOMA             0            119
  OLIGODENDROGLIOMA            0            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V6, binary
                cls
clus               0   1
  RGS3 MUTATED     1   4
  RGS3 WILD-TYPE  91 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      1    4
  RGS3 WILD-TYPE   91  377
     clus
vv    RGS3 MUTATED RGS3 WILD-TYPE
  NO             1             91
  YES            4            377
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS3 MUTATED                                  0     0
  RGS3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RGS3 MUTATED                           0     5
  RGS3 WILD-TYPE                        15   433
D143V7, multiclass
                                  clus
vv                                 RGS3 MUTATED RGS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              8
  BLACK OR AFRICAN AMERICAN                   0             15
  WHITE                                       5            433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V8, binary
                cls
clus               0   1
  RGS3 MUTATED     1   4
  RGS3 WILD-TYPE  17 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      1    4
  RGS3 WILD-TYPE   17  416
                        clus
vv                       RGS3 MUTATED RGS3 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            4            416
[1] 2 2
[1] FALSE
