[1] "ofn"        "-oTPAAD-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/PAAD-TP/15087151/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/15182489/transformed.cor.cli.txt"

nPatients in clinical file=174, in cluster file=146, common to both=136
[1] "Reduce the number of clustering variables from 201 to 188."
[1] 188 136
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           114             22 
  KRAS MUTATED KRAS WILD-TYPE 
           114             22 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            91             45 
  TP53 MUTATED TP53 WILD-TYPE 
            91             45 
[1] "JMY MUTATION ANALYSIS"
[1] 3
  JMY MUTATED JMY WILD-TYPE 
           51            85 
  JMY MUTATED JMY WILD-TYPE 
           51            85 
[1] "RIOK1 MUTATION ANALYSIS"
[1] 3
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             50              86 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             50              86 
[1] "LCE2A MUTATION ANALYSIS"
[1] 3
  LCE2A MUTATED LCE2A WILD-TYPE 
             43              93 
  LCE2A MUTATED LCE2A WILD-TYPE 
             43              93 
[1] "C1QB MUTATION ANALYSIS"
[1] 3
  C1QB MUTATED C1QB WILD-TYPE 
            33            103 
  C1QB MUTATED C1QB WILD-TYPE 
            33            103 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              28              108 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              28              108 
[1] "AEBP1 MUTATION ANALYSIS"
[1] 3
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             25             111 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             25             111 
[1] "RBM47 MUTATION ANALYSIS"
[1] 3
  RBM47 MUTATED RBM47 WILD-TYPE 
             25             111 
  RBM47 MUTATED RBM47 WILD-TYPE 
             25             111 
[1] "ANKRD36 MUTATION ANALYSIS"
[1] 3
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               113 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               113 
[1] "RFX1 MUTATION ANALYSIS"
[1] 3
  RFX1 MUTATED RFX1 WILD-TYPE 
            23            113 
  RFX1 MUTATED RFX1 WILD-TYPE 
            23            113 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             13             123 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             13             123 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             28             108 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             28             108 
[1] "GPR6 MUTATION ANALYSIS"
[1] 3
  GPR6 MUTATED GPR6 WILD-TYPE 
            12            124 
  GPR6 MUTATED GPR6 WILD-TYPE 
            12            124 
[1] "LZTS1 MUTATION ANALYSIS"
[1] 3
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              8             128 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              8             128 
[1] "NCOA3 MUTATION ANALYSIS"
[1] 3
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             13             123 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             13             123 
[1] "SIK3 MUTATION ANALYSIS"
[1] 3
  SIK3 MUTATED SIK3 WILD-TYPE 
            12            124 
  SIK3 MUTATED SIK3 WILD-TYPE 
            12            124 
[1] "ZMIZ2 MUTATION ANALYSIS"
[1] 3
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             124 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             124 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            14            122 
  IRS4 MUTATED IRS4 WILD-TYPE 
            14            122 
[1] "ESPN MUTATION ANALYSIS"
[1] 3
  ESPN MUTATED ESPN WILD-TYPE 
             5            131 
  ESPN MUTATED ESPN WILD-TYPE 
             5            131 
[1] "ATP2C1 MUTATION ANALYSIS"
[1] 3
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              128 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              128 
[1] "FNDC1 MUTATION ANALYSIS"
[1] 3
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             13             123 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             13             123 
[1] "TMEM91 MUTATION ANALYSIS"
[1] 3
  TMEM91 MUTATED TMEM91 WILD-TYPE 
               6              130 
  TMEM91 MUTATED TMEM91 WILD-TYPE 
               6              130 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               11               125 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               11               125 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              127 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              127 
[1] "OGFOD1 MUTATION ANALYSIS"
[1] 3
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               4              132 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               4              132 
[1] "DCP1B MUTATION ANALYSIS"
[1] 3
  DCP1B MUTATED DCP1B WILD-TYPE 
              7             129 
  DCP1B MUTATED DCP1B WILD-TYPE 
              7             129 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
             5            131 
  RBMX MUTATED RBMX WILD-TYPE 
             5            131 
[1] "ZNF880 MUTATION ANALYSIS"
[1] 3
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               3              133 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               3              133 
[1] "UBAC1 MUTATION ANALYSIS"
[1] 3
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             131 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             131 
[1] "CASQ2 MUTATION ANALYSIS"
[1] 3
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              7             129 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              7             129 
[1] "ZNF678 MUTATION ANALYSIS"
[1] 3
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              131 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              131 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             131 
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             131 
[1] "VWA3A MUTATION ANALYSIS"
[1] 3
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             131 
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             131 
[1] "NBPF16 MUTATION ANALYSIS"
[1] 3
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               6              130 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               6              130 
[1] "PARP10 MUTATION ANALYSIS"
[1] 3
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              131 
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              131 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              128 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              128 
[1] "HACL1 MUTATION ANALYSIS"
[1] 3
  HACL1 MUTATED HACL1 WILD-TYPE 
              4             132 
  HACL1 MUTATED HACL1 WILD-TYPE 
              4             132 
[1] "PRKRA MUTATION ANALYSIS"
[1] 3
  PRKRA MUTATED PRKRA WILD-TYPE 
              3             133 
  PRKRA MUTATED PRKRA WILD-TYPE 
              3             133 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               5              131 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               5              131 
[1] "CD86 MUTATION ANALYSIS"
[1] 3
  CD86 MUTATED CD86 WILD-TYPE 
             6            130 
  CD86 MUTATED CD86 WILD-TYPE 
             6            130 
[1] "RNF32 MUTATION ANALYSIS"
[1] 3
  RNF32 MUTATED RNF32 WILD-TYPE 
              4             132 
  RNF32 MUTATED RNF32 WILD-TYPE 
              4             132 
[1] "SDCBP MUTATION ANALYSIS"
[1] 3
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             130 
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             130 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             129 
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             129 
[1] "NLRP2 MUTATION ANALYSIS"
[1] 3
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              5             131 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              5             131 
[1] "PLIN4 MUTATION ANALYSIS"
[1] 3
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              6             130 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              6             130 
[1] "CBX3 MUTATION ANALYSIS"
[1] 3
  CBX3 MUTATED CBX3 WILD-TYPE 
             3            133 
  CBX3 MUTATED CBX3 WILD-TYPE 
             3            133 
[1] "SUZ12 MUTATION ANALYSIS"
[1] 3
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             132 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             132 
[1] "MTBP MUTATION ANALYSIS"
[1] 3
  MTBP MUTATED MTBP WILD-TYPE 
             3            133 
  MTBP MUTATED MTBP WILD-TYPE 
             3            133 
[1] "SYT14 MUTATION ANALYSIS"
[1] 3
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             132 
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             132 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
              7             129 
  RNF43 MUTATED RNF43 WILD-TYPE 
              7             129 
[1] "AAK1 MUTATION ANALYSIS"
[1] 3
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            132 
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            132 
[1] "HSPE1 MUTATION ANALYSIS"
[1] 3
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             132 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             132 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             129 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             129 
[1] "CFTR MUTATION ANALYSIS"
[1] 3
  CFTR MUTATED CFTR WILD-TYPE 
             7            129 
  CFTR MUTATED CFTR WILD-TYPE 
             7            129 
[1] "NAA20 MUTATION ANALYSIS"
[1] 3
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             133 
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             133 
[1] "TRPC4 MUTATION ANALYSIS"
[1] 3
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             130 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             130 
[1] "CHRNA9 MUTATION ANALYSIS"
[1] 3
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              132 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              132 
[1] "SP140 MUTATION ANALYSIS"
[1] 3
  SP140 MUTATED SP140 WILD-TYPE 
              5             131 
  SP140 MUTATED SP140 WILD-TYPE 
              5             131 
[1] "KCNA7 MUTATION ANALYSIS"
[1] 3
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             131 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             131 
[1] "AQP7 MUTATION ANALYSIS"
[1] 3
  AQP7 MUTATED AQP7 WILD-TYPE 
             7            129 
  AQP7 MUTATED AQP7 WILD-TYPE 
             7            129 
[1] "SKA3 MUTATION ANALYSIS"
[1] 3
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            130 
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            130 
[1] "DAAM1 MUTATION ANALYSIS"
[1] 3
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             130 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             130 
[1] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            132 
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            132 
[1] "NUP210L MUTATION ANALYSIS"
[1] 3
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               131 
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               131 
[1] "GPR98 MUTATION ANALYSIS"
[1] 3
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             128 
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             128 
[1] "CD2AP MUTATION ANALYSIS"
[1] 3
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             133 
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             133 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             127 
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             127 
[1] "KIAA0586 MUTATION ANALYSIS"
[1] 3
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                130 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                130 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             8            128 
  GNAS MUTATED GNAS WILD-TYPE 
             8            128 
[1] "FAR1 MUTATION ANALYSIS"
[1] 3
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            132 
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            132 
[1] "OR2T4 MUTATION ANALYSIS"
[1] 3
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              4             132 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              4             132 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             131 
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             131 
[1] "TAX1BP1 MUTATION ANALYSIS"
[1] 3
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               131 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               131 
[1] "CCDC33 MUTATION ANALYSIS"
[1] 3
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              133 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              133 
[1] "JAK2 MUTATION ANALYSIS"
[1] 3
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            132 
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            132 
[1] "COL28A1 MUTATION ANALYSIS"
[1] 3
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               131 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               131 
[1] "KLHL20 MUTATION ANALYSIS"
[1] 3
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              133 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              133 
[1] "WRN MUTATION ANALYSIS"
[1] 3
  WRN MUTATED WRN WILD-TYPE 
            4           132 
  WRN MUTATED WRN WILD-TYPE 
            4           132 
[1] "P2RY1 MUTATION ANALYSIS"
[1] 3
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             131 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             131 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            132 
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            132 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              130 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              130 
[1] "MORF4L1 MUTATION ANALYSIS"
[1] 3
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               133 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               133 
[1] "SEPHS2 MUTATION ANALYSIS"
[1] 3
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              131 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              131 
[1] "HELZ MUTATION ANALYSIS"
[1] 3
  HELZ MUTATED HELZ WILD-TYPE 
             5            131 
  HELZ MUTATED HELZ WILD-TYPE 
             5            131 
[1] "DOCK8 MUTATION ANALYSIS"
[1] 3
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              4             132 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              4             132 
[1] "KLK13 MUTATION ANALYSIS"
[1] 3
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             131 
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             131 
[1] "OXR1 MUTATION ANALYSIS"
[1] 3
  OXR1 MUTATED OXR1 WILD-TYPE 
             4            132 
  OXR1 MUTATED OXR1 WILD-TYPE 
             4            132 
[1] "OR52D1 MUTATION ANALYSIS"
[1] 3
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              132 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              132 
[1] "CSTF2T MUTATION ANALYSIS"
[1] 3
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              133 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              133 
[1] "AP3B1 MUTATION ANALYSIS"
[1] 3
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             132 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             132 
[1] "OMA1 MUTATION ANALYSIS"
[1] 3
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            133 
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            133 
[1] "IYD MUTATION ANALYSIS"
[1] 3
  IYD MUTATED IYD WILD-TYPE 
            6           130 
  IYD MUTATED IYD WILD-TYPE 
            6           130 
[1] "PRSS3 MUTATION ANALYSIS"
[1] 3
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             133 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             133 
[1] "COBL MUTATION ANALYSIS"
[1] 3
  COBL MUTATED COBL WILD-TYPE 
             6            130 
  COBL MUTATED COBL WILD-TYPE 
             6            130 
[1] "SORT1 MUTATION ANALYSIS"
[1] 3
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             131 
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             131 
[1] "SSBP3 MUTATION ANALYSIS"
[1] 3
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             133 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             133 
[1] "GPSM2 MUTATION ANALYSIS"
[1] 3
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             133 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             133 
[1] "EEF2 MUTATION ANALYSIS"
[1] 3
  EEF2 MUTATED EEF2 WILD-TYPE 
             5            131 
  EEF2 MUTATED EEF2 WILD-TYPE 
             5            131 
[1] "ZACN MUTATION ANALYSIS"
[1] 3
  ZACN MUTATED ZACN WILD-TYPE 
             3            133 
  ZACN MUTATED ZACN WILD-TYPE 
             3            133 
[1] "ZMYM2 MUTATION ANALYSIS"
[1] 3
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             133 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             133 
[1] "GSN MUTATION ANALYSIS"
[1] 3
  GSN MUTATED GSN WILD-TYPE 
            4           132 
  GSN MUTATED GSN WILD-TYPE 
            4           132 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              128 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              128 
[1] "MLPH MUTATION ANALYSIS"
[1] 3
  MLPH MUTATED MLPH WILD-TYPE 
             3            133 
  MLPH MUTATED MLPH WILD-TYPE 
             3            133 
[1] "UBXN4 MUTATION ANALYSIS"
[1] 3
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             133 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             133 
[1] "KCNE1 MUTATION ANALYSIS"
[1] 3
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             132 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             132 
[1] "RTTN MUTATION ANALYSIS"
[1] 3
  RTTN MUTATED RTTN WILD-TYPE 
             5            131 
  RTTN MUTATED RTTN WILD-TYPE 
             5            131 
[1] "FAM8A1 MUTATION ANALYSIS"
[1] 3
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              132 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              132 
[1] "ACTRT2 MUTATION ANALYSIS"
[1] 3
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              133 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              133 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             129 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             129 
[1] "OR1N2 MUTATION ANALYSIS"
[1] 3
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              4             132 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              4             132 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            133 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            133 
[1] "MIPEP MUTATION ANALYSIS"
[1] 3
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             133 
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             133 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                133 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                133 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              129 
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              129 
[1] "POM121 MUTATION ANALYSIS"
[1] 3
  POM121 MUTATED POM121 WILD-TYPE 
               4              132 
  POM121 MUTATED POM121 WILD-TYPE 
               4              132 
[1] "LCP2 MUTATION ANALYSIS"
[1] 3
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            133 
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            133 
[1] "L1CAM MUTATION ANALYSIS"
[1] 3
  L1CAM MUTATED L1CAM WILD-TYPE 
              5             131 
  L1CAM MUTATED L1CAM WILD-TYPE 
              5             131 
[1] "ABCG5 MUTATION ANALYSIS"
[1] 3
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              3             133 
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              3             133 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            131 
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            131 
[1] "ZNF780A MUTATION ANALYSIS"
[1] 3
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               131 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               131 
[1] "DDX4 MUTATION ANALYSIS"
[1] 3
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            131 
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            131 
[1] "BTN2A1 MUTATION ANALYSIS"
[1] 3
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              133 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              133 
[1] "TDRD5 MUTATION ANALYSIS"
[1] 3
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             132 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             132 
[1] "OR2A14 MUTATION ANALYSIS"
[1] 3
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               3              133 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               3              133 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             131 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             131 
[1] "SEPT2 MUTATION ANALYSIS"
[1] 3
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             133 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             133 
[1] "WDHD1 MUTATION ANALYSIS"
[1] 3
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             133 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             133 
[1] "ANKRD49 MUTATION ANALYSIS"
[1] 3
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               133 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               133 
[1] "PAPSS2 MUTATION ANALYSIS"
[1] 3
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              132 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              132 
[1] "GPRC6A MUTATION ANALYSIS"
[1] 3
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              131 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              131 
[1] "PDXDC1 MUTATION ANALYSIS"
[1] 3
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              133 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              133 
[1] "TGM5 MUTATION ANALYSIS"
[1] 3
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            132 
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            132 
[1] "NUP54 MUTATION ANALYSIS"
[1] 3
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             133 
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             133 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             133 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             133 
[1] "DHX35 MUTATION ANALYSIS"
[1] 3
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             132 
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             132 
[1] "CEACAM4 MUTATION ANALYSIS"
[1] 3
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                3               133 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                3               133 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             133 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             133 
[1] "SYCP2 MUTATION ANALYSIS"
[1] 3
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             131 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             131 
[1] "LACTB MUTATION ANALYSIS"
[1] 3
  LACTB MUTATED LACTB WILD-TYPE 
              3             133 
  LACTB MUTATED LACTB WILD-TYPE 
              3             133 
[1] "TEKT4 MUTATION ANALYSIS"
[1] 3
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             130 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             130 
[1] "MC3R MUTATION ANALYSIS"
[1] 3
  MC3R MUTATED MC3R WILD-TYPE 
             4            132 
  MC3R MUTATED MC3R WILD-TYPE 
             4            132 
[1] "CSRNP3 MUTATION ANALYSIS"
[1] 3
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               4              132 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               4              132 
[1] "PHF15 MUTATION ANALYSIS"
[1] 3
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             132 
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             132 
[1] "ZBTB4 MUTATION ANALYSIS"
[1] 3
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              3             133 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              3             133 
[1] "RSPO1 MUTATION ANALYSIS"
[1] 3
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             133 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             133 
[1] "WWP2 MUTATION ANALYSIS"
[1] 3
  WWP2 MUTATED WWP2 WILD-TYPE 
             5            131 
  WWP2 MUTATED WWP2 WILD-TYPE 
             5            131 
[1] "CPNE2 MUTATION ANALYSIS"
[1] 3
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             133 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             133 
[1] "WDR36 MUTATION ANALYSIS"
[1] 3
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             133 
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             133 
[1] "CYTH4 MUTATION ANALYSIS"
[1] 3
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             133 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             133 
[1] "BOC MUTATION ANALYSIS"
[1] 3
  BOC MUTATED BOC WILD-TYPE 
            4           132 
  BOC MUTATED BOC WILD-TYPE 
            4           132 
[1] "C5ORF51 MUTATION ANALYSIS"
[1] 3
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               133 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               133 
[1] "LILRB2 MUTATION ANALYSIS"
[1] 3
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              132 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              132 
[1] "FLVCR1 MUTATION ANALYSIS"
[1] 3
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              133 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              133 
[1] "ZNF483 MUTATION ANALYSIS"
[1] 3
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              132 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              132 
[1] "NDUFV2 MUTATION ANALYSIS"
[1] 3
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              133 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              133 
[1] "PSMB4 MUTATION ANALYSIS"
[1] 3
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             132 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             132 
[1] "KIAA1045 MUTATION ANALYSIS"
[1] 3
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
                 5                131 
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
                 5                131 
[1] "KLK15 MUTATION ANALYSIS"
[1] 3
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             131 
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             131 
[1] "ZNF660 MUTATION ANALYSIS"
[1] 3
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               3              133 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               3              133 
[1] "CCDC87 MUTATION ANALYSIS"
[1] 3
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              133 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              133 
[1] "KIF4B MUTATION ANALYSIS"
[1] 3
  KIF4B MUTATED KIF4B WILD-TYPE 
              4             132 
  KIF4B MUTATED KIF4B WILD-TYPE 
              4             132 
[1] "ENPP7 MUTATION ANALYSIS"
[1] 3
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             131 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             131 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              130 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              130 
[1] "NAA40 MUTATION ANALYSIS"
[1] 3
  NAA40 MUTATED NAA40 WILD-TYPE 
              3             133 
  NAA40 MUTATED NAA40 WILD-TYPE 
              3             133 
[1] "AKAP13 MUTATION ANALYSIS"
[1] 3
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               6              130 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               6              130 
[1] "ASH1L MUTATION ANALYSIS"
[1] 3
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             130 
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             130 
[1] "ATP2C2 MUTATION ANALYSIS"
[1] 3
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              132 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              132 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                128 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                128 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
              6             130 
  MKI67 MUTATED MKI67 WILD-TYPE 
              6             130 
[1] "FCGBP MUTATION ANALYSIS"
[1] 3
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             124 
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             124 
[1] "SRFBP1 MUTATION ANALYSIS"
[1] 3
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              133 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              133 
[1] "NFKBIZ MUTATION ANALYSIS"
[1] 3
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               4              132 
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               4              132 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               5              131 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               5              131 
[1] "ZNF358 MUTATION ANALYSIS"
[1] 3
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              132 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              132 
[1] "HIST1H2BK MUTATION ANALYSIS"
[1] 3
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  3                 133 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  3                 133 
[1] "DDB1 MUTATION ANALYSIS"
[1] 3
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            131 
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            131 
[1] "BVES MUTATION ANALYSIS"
[1] 3
  BVES MUTATED BVES WILD-TYPE 
             4            132 
  BVES MUTATED BVES WILD-TYPE 
             4            132 
[1] "SLC26A3 MUTATION ANALYSIS"
[1] 3
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                3               133 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                3               133 
[1] "CMYA5 MUTATION ANALYSIS"
[1] 3
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              7             129 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              7             129 
[1] "CHSY3 MUTATION ANALYSIS"
[1] 3
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              5             131 
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              5             131 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             129 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             129 
[1] "NGF MUTATION ANALYSIS"
[1] 3
  NGF MUTATED NGF WILD-TYPE 
            4           132 
  NGF MUTATED NGF WILD-TYPE 
            4           132 
[1] "SARS2 MUTATION ANALYSIS"
[1] 3
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             133 
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             133 
[1] "ADORA3 MUTATION ANALYSIS"
[1] 3
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              131 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              131 
[1] "ATP11B MUTATION ANALYSIS"
[1] 3
  ATP11B MUTATED ATP11B WILD-TYPE 
               4              132 
  ATP11B MUTATED ATP11B WILD-TYPE 
               4              132 
[1] "RAG1 MUTATION ANALYSIS"
[1] 3
  RAG1 MUTATED RAG1 WILD-TYPE 
             3            133 
  RAG1 MUTATED RAG1 WILD-TYPE 
             3            133 
[1] "HK2 MUTATION ANALYSIS"
[1] 3
  HK2 MUTATED HK2 WILD-TYPE 
            4           132 
  HK2 MUTATED HK2 WILD-TYPE 
            4           132 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "NUMBER_PACK_YEARS_SMOKED"              
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 136 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=68,	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=80,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'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 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 136 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "COMPLETENESS_OF_RESECTION"    
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=44, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  5  13 115   3 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    5    13   118 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  5  13 115   3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    5    13   118 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=27, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   49 63
  KRAS WILD-TYPE 13  9
  KRAS MUTATED KRAS WILD-TYPE 
           112             22 
  KRAS MUTATED KRAS WILD-TYPE 
            63              9 
$`KRAS MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       34.09        10.13        75.12        71.74        10.98         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU 
        3.12        17.00        24.07        14.76         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G 
       12.03         0.69         3.95         9.83        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
       15.81        19.66         3.85        17.16        12.00        15.85 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        7.40         8.05        10.29        19.20         8.78        15.45 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XD-AAUL 
       22.85        16.80         0.39        13.81        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

$`KRAS WILD-TYPE`
TCGA-2J-AABA TCGA-3A-A9I5 TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 
       19.96        53.00        12.39        19.27         5.88        11.93 
TCGA-FB-A78T TCGA-FB-AAPY TCGA-HZ-8317 TCGA-HZ-8519 TCGA-IB-7888 TCGA-IB-7891 
       12.43        34.82        12.43        14.93        43.79        21.30 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 
       15.98         2.47         7.20         9.44        12.92        12.46 
TCGA-Q3-A5QY TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUH 
       13.68        27.75        14.14        12.99 

  KRAS MUTATED KRAS WILD-TYPE 
          0.13           2.47 
  KRAS MUTATED KRAS WILD-TYPE 
         75.12          53.00 
  KRAS MUTATED KRAS WILD-TYPE 
        13.825         13.335 
[1] "0.1 - 75.1 (13.8)" "2.5 - 53.0 (13.3)"
[1] "hr=" "1.6"
D1V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KRAS MUTATED          2        5        16        85         3        3
  KRAS WILD-TYPE        2        1         4        14         1        0
D1V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE IA             2              2
  STAGE IB             5              1
  STAGE IIA           16              4
  STAGE IIB           85             14
  STAGE III            3              1
  STAGE IV             3              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  KRAS MUTATED     3  10   101
  KRAS WILD-TYPE   2   3    17
D1V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               3              2
  T2              10              3
  T3+T4          101             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  KRAS MUTATED   25 89
  KRAS WILD-TYPE  7 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     25   89
  KRAS WILD-TYPE    7   15
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           25              7
  1           89             15
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  KRAS MUTATED   52  3
  KRAS WILD-TYPE 10  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     52    3
  KRAS WILD-TYPE   10    0
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           52             10
  1            3              0
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  KRAS MUTATED   51 63
  KRAS WILD-TYPE 11 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     51   63
  KRAS WILD-TYPE   11   11
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           51             11
  MALE             63             11
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRAS MUTATED                                   104
  KRAS WILD-TYPE                                  18
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRAS MUTATED                                       9
  KRAS WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRAS MUTATED                                                  0
  KRAS WILD-TYPE                                                2
D1V8, multiclass
                                                  clus
vv                                                 KRAS MUTATED KRAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       104             18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       9              2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
D1V10, continuous
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   63 42  0  3
  KRAS WILD-TYPE 14  6  1  0
D1V11, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           63             14
  R1           42              6
  R2            0              1
  RX            3              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       2                         2   106
  KRAS WILD-TYPE     0                         3    19
D1V13, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                              106             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                cls
clus              0  1
  KRAS MUTATED    3 83
  KRAS WILD-TYPE  0 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3   83
  KRAS WILD-TYPE    0   21
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                3              0
  NOT HISPANIC OR LATINO           83             21
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   38 52
  TP53 WILD-TYPE 24 20
  TP53 MUTATED TP53 WILD-TYPE 
            90             44 
  TP53 MUTATED TP53 WILD-TYPE 
            52             20 
$`TP53 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABF 
        2.17        23.97         9.63         2.63        20.61        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.26        15.91        14.47        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 
        4.70        22.49         3.39        12.95         9.60        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 
        7.36        24.26        28.73        15.06        10.13        12.39 
TCGA-F2-6879 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPS 
       10.98         3.12        17.00        24.07        12.43         7.50 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       34.82        23.54        15.55         5.03        12.89        13.84 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
        0.13        20.19        23.21         0.69         3.95         9.83 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.92        21.70        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         1.08        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.35        23.80         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
       19.66         3.85        17.16        12.00        15.85        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUP 
       20.88        21.90         1.35        15.88         4.73        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 
        6.02         7.40         8.05        12.92        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-RB-AA9M TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 
        8.78        15.45         9.40        17.26        22.85        16.80 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.81        12.99        12.03        13.32        12.76         0.69 

$`TP53 WILD-TYPE`
TCGA-2J-AABA TCGA-2J-AABE TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IX TCGA-3E-AAAY 
       19.96        22.22        53.00        23.61        34.09        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM 
       71.74         7.66        19.27         5.88        11.93        14.76 
TCGA-FB-AAPU TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-HZ-7919 TCGA-HZ-7926 TCGA-HZ-8002 
       12.53         4.04         1.02        19.50        17.03        12.03 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7885 
       12.43        14.93        16.14         0.23        19.82        41.33 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-A7LX TCGA-IB-AAUM 
       21.30        15.98         2.47         7.20         8.22         0.26 
TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.86        11.11         9.44        12.46        13.68         3.12 
TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G 
       15.32        21.24        23.08        27.75        14.14         0.39 
TCGA-YB-A89D TCGA-YY-A8LH 
       11.51        66.28 

  TP53 MUTATED TP53 WILD-TYPE 
          0.13           0.23 
  TP53 MUTATED TP53 WILD-TYPE 
         49.38          75.12 
  TP53 MUTATED TP53 WILD-TYPE 
        13.155         14.450 
[1] "0.1 - 49.4 (13.2)" "0.2 - 75.1 (14.4)"
[1] "hr=" "1.6"
D2V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TP53 MUTATED          1        2        14        68         3        3
  TP53 WILD-TYPE        3        4         6        31         1        0
D2V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE IA             1              3
  STAGE IB             2              4
  STAGE IIA           14              6
  STAGE IIB           68             31
  STAGE III            3              1
  STAGE IV             3              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TP53 MUTATED    2  8    81
  TP53 WILD-TYPE  3  5    37
D2V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               2              3
  T2               8              5
  T3+T4           81             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                cls
clus              0  1
  TP53 MUTATED   20 71
  TP53 WILD-TYPE 12 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     20   71
  TP53 WILD-TYPE   12   33
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           20             12
  1           71             33
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus              0  1
  TP53 MUTATED   46  3
  TP53 WILD-TYPE 16  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     46    3
  TP53 WILD-TYPE   16    0
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           46             16
  1            3              0
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus              0  1
  TP53 MUTATED   43 48
  TP53 WILD-TYPE 19 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     43   48
  TP53 WILD-TYPE   19   26
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           43             19
  MALE             48             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TP53 MUTATED                                    82
  TP53 WILD-TYPE                                  40
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TP53 MUTATED                                       8
  TP53 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TP53 MUTATED                                                  0
  TP53 WILD-TYPE                                                2
D2V8, multiclass
                                                  clus
vv                                                 TP53 MUTATED TP53 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        82             40
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       8              3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, continuous
D2V10, continuous
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   48 37  1  1
  TP53 WILD-TYPE 29 11  0  2
D2V11, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           48             29
  R1           37             11
  R2            1              0
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       1                         2    84
  TP53 WILD-TYPE     1                         3    41
D2V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               84             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                cls
clus              0  1
  TP53 MUTATED    2 63
  TP53 WILD-TYPE  1 41
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2   63
  TP53 WILD-TYPE    1   41
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                2              1
  NOT HISPANIC OR LATINO           63             41
[1] 2 2
[1] FALSE

Clustering(3) Variable = JMY MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  JMY MUTATED   24 27
  JMY WILD-TYPE 38 45
  JMY MUTATED JMY WILD-TYPE 
           51            83 
  JMY MUTATED JMY WILD-TYPE 
           27            45 
$`JMY MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABA TCGA-2J-AABE TCGA-3A-A9IB TCGA-3A-A9IZ TCGA-3A-A9J0 
       23.97        19.96        22.22         7.36        10.13        12.39 
TCGA-F2-6879 TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
       10.98        19.27        24.07        12.43        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03        12.89        13.84 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 
        0.13        20.19        17.03        23.21         9.83        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7646 
       21.70        16.14         6.38         5.26         0.23         4.77 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7887 TCGA-IB-8126 TCGA-IB-8127 
       15.35        19.82        23.80         3.62         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-M8-A5N4 
       12.00        15.85         1.35        15.88         8.05        19.20 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-S4-A8RM TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
        8.78        13.68        21.24        16.80        14.14         0.39 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YH-A8SY 
       12.99        12.03        12.76 

$`JMY WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH 
        2.17         9.63         2.63        20.61        22.72        22.26 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3E-AAAY 
       20.84        24.26        28.73        15.06        34.09        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       71.74         7.66         3.12        17.00         5.88        11.93 
TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAQ3 TCGA-HZ-7919 TCGA-HZ-8002 TCGA-HZ-8003 
       14.76         7.50         1.02        19.50        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77P 
        3.95        12.43        14.93        10.13        21.60        10.85 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7886 
        1.08        12.95        49.38        21.90        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM 
        7.20        15.12        20.88        21.90         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-Q3-AA2A 
        9.44        12.92        12.46        10.29        15.45         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
       15.32         9.40        17.26        23.08        22.85        27.75 
TCGA-XD-AAUG TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.81        13.32        11.51        66.28         0.69 

  JMY MUTATED JMY WILD-TYPE 
         0.13          0.26 
  JMY MUTATED JMY WILD-TYPE 
        34.82         75.12 
  JMY MUTATED JMY WILD-TYPE 
        13.68         13.81 
[1] "0.1 - 34.8 (13.7)" "0.3 - 75.1 (13.8)"
[1] "hr=" "1.2"
D3V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  JMY MUTATED          0        1         8        38         3        1
  JMY WILD-TYPE        4        5        12        61         1        2
D3V3, multiclass
           clus
vv          JMY MUTATED JMY WILD-TYPE
  STAGE IA            0             4
  STAGE IB            1             5
  STAGE IIA           8            12
  STAGE IIB          38            61
  STAGE III           3             1
  STAGE IV            1             2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  JMY MUTATED    0  6    45
  JMY WILD-TYPE  5  7    73
D3V4, multiclass
       clus
vv      JMY MUTATED JMY WILD-TYPE
  T1              0             5
  T2              6             7
  T3+T4          45            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
               cls
clus             0  1
  JMY MUTATED   11 40
  JMY WILD-TYPE 21 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     11   40
  JMY WILD-TYPE   21   64
   clus
vv  JMY MUTATED JMY WILD-TYPE
  0          11            21
  1          40            64
[1] 2 2
[1] FALSE
D3V6, binary
               cls
clus             0  1
  JMY MUTATED   22  1
  JMY WILD-TYPE 40  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     22    1
  JMY WILD-TYPE   40    2
   clus
vv  JMY MUTATED JMY WILD-TYPE
  0          22            40
  1           1             2
[1] 2 2
[1] FALSE
D3V7, binary
               cls
clus             0  1
  JMY MUTATED   23 28
  JMY WILD-TYPE 39 46
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     23   28
  JMY WILD-TYPE   39   46
        clus
vv       JMY MUTATED JMY WILD-TYPE
  FEMALE          23            39
  MALE            28            46
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  JMY MUTATED                                    46
  JMY WILD-TYPE                                  76
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  JMY MUTATED                                       4
  JMY WILD-TYPE                                     7
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  JMY MUTATED                                                  0
  JMY WILD-TYPE                                                2
D3V8, multiclass
                                                  clus
vv                                                 JMY MUTATED JMY WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       46            76
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      4             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, continuous
               vv
clus            R0 R1 R2 RX
  JMY MUTATED   26 20  1  1
  JMY WILD-TYPE 51 28  0  2
D3V11, multiclass
    clus
vv   JMY MUTATED JMY WILD-TYPE
  R0          26            51
  R1          20            28
  R2           1             0
  RX           1             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JMY MUTATED       2                         1    46
  JMY WILD-TYPE     0                         4    79
D3V13, multiclass
                           clus
vv                          JMY MUTATED JMY WILD-TYPE
  ASIAN                               2             0
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                              46            79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
               cls
clus             0  1
  JMY MUTATED    1 41
  JMY WILD-TYPE  2 63
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED      1   41
  JMY WILD-TYPE    2   63
                        clus
vv                       JMY MUTATED JMY WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          41            63
[1] 2 2
[1] FALSE

Clustering(4) Variable = RIOK1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  RIOK1 MUTATED   24 25
  RIOK1 WILD-TYPE 38 47
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             49              85 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             25              47 
$`RIOK1 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       23.97        22.72        15.91        14.40         9.11        21.44 
TCGA-2L-AAQI TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3E-AAAY TCGA-FB-A4P5 
        3.39         7.36        28.73        15.06        75.12         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-H6-A45N 
       24.07        14.76        12.43        12.53        23.54        13.84 
TCGA-HZ-7922 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A77O 
        0.13         0.69        12.43        21.70         6.38         5.26 
TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       10.85        12.95         4.77        21.90        15.35        19.82 
TCGA-IB-7885 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
       41.33        43.79        19.66        21.30         2.47        17.16 
TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.86         6.02         9.44         8.05        10.29        19.20 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 
       15.45         3.12        15.32         9.40        27.75        16.80 
TCGA-Z5-AAPL 
        0.69 

$`RIOK1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
       22.26        14.47         4.70        22.49        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IX TCGA-3A-A9IZ 
       53.00        23.61        20.84        24.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       12.39        71.74        10.98         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P6 TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       17.00        11.93         7.50        34.82        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 
        5.03         1.02        12.89        19.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 
       23.21        12.03         3.95         9.83        14.93        17.92 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 
       16.14        10.13        21.60         1.08         0.23        49.38 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-7897 
       23.80         4.04         3.62        15.81         3.85        15.98 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         4.73        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
       11.11         7.40        12.92        12.46         8.78        13.68 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A77E TCGA-US-A77G 
       21.24        17.26        23.08        22.85        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  RIOK1 MUTATED RIOK1 WILD-TYPE 
           0.13            0.23 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
          75.12           71.74 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
          14.40           13.32 
[1] "0.1 - 75.1 (14.4)" "0.2 - 71.7 (13.3)"
[1] "hr=" "1.1"
D4V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RIOK1 MUTATED          1        3         6        38         1        1
  RIOK1 WILD-TYPE        3        3        14        61         3        2
D4V3, multiclass
           clus
vv          RIOK1 MUTATED RIOK1 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              3               3
  STAGE IIA             6              14
  STAGE IIB            38              61
  STAGE III             1               3
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RIOK1 MUTATED    2  7    41
  RIOK1 WILD-TYPE  3  6    77
D4V4, multiclass
       clus
vv      RIOK1 MUTATED RIOK1 WILD-TYPE
  T1                2               3
  T2                7               6
  T3+T4            41              77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                 cls
clus               0  1
  RIOK1 MUTATED    9 41
  RIOK1 WILD-TYPE 23 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      9   41
  RIOK1 WILD-TYPE   23   63
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0             9              23
  1            41              63
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus               0  1
  RIOK1 MUTATED   25  1
  RIOK1 WILD-TYPE 37  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     25    1
  RIOK1 WILD-TYPE   37    2
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0            25              37
  1             1               2
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus               0  1
  RIOK1 MUTATED   29 21
  RIOK1 WILD-TYPE 33 53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     29   21
  RIOK1 WILD-TYPE   33   53
        clus
vv       RIOK1 MUTATED RIOK1 WILD-TYPE
  FEMALE            29              33
  MALE              21              53
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RIOK1 MUTATED                                    44
  RIOK1 WILD-TYPE                                  78
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RIOK1 MUTATED                                       4
  RIOK1 WILD-TYPE                                     7
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RIOK1 MUTATED                                                  2
  RIOK1 WILD-TYPE                                                0
D4V8, multiclass
                                                  clus
vv                                                 RIOK1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         44
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             2
                                                  clus
vv                                                 RIOK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           78
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, continuous
D4V10, continuous
                 vv
clus              R0 R1 R2 RX
  RIOK1 MUTATED   27 18  0  1
  RIOK1 WILD-TYPE 50 30  1  2
D4V11, multiclass
    clus
vv   RIOK1 MUTATED RIOK1 WILD-TYPE
  R0            27              50
  R1            18              30
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIOK1 MUTATED       1                         1    45
  RIOK1 WILD-TYPE     1                         4    80
D4V13, multiclass
                           clus
vv                          RIOK1 MUTATED RIOK1 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                45              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                 cls
clus               0  1
  RIOK1 MUTATED    1 38
  RIOK1 WILD-TYPE  2 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      1   38
  RIOK1 WILD-TYPE    2   66
                        clus
vv                       RIOK1 MUTATED RIOK1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            38              66
[1] 2 2
[1] FALSE

Clustering(5) Variable = LCE2A MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  LCE2A MUTATED   17 26
  LCE2A WILD-TYPE 45 46
  LCE2A MUTATED LCE2A WILD-TYPE 
             43              91 
  LCE2A MUTATED LCE2A WILD-TYPE 
             26              46 
$`LCE2A MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABO TCGA-2J-AABV 
        2.17         9.63        20.61        19.96        14.47        21.44 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I9 TCGA-3A-A9IX TCGA-F2-6879 TCGA-FB-A4P6 
        3.39        12.95        20.84        34.09        10.98        11.93 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.43         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ3 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-A49H 
        1.02        20.19        17.03         9.83        12.43        16.14 
TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-A6UG 
       12.95         4.04         3.62        15.81         3.85         1.35 
TCGA-IB-AAUP TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-RB-A7B8 
       14.17         8.05        12.92        12.46        19.20        15.32 
TCGA-RB-AA9M TCGA-S4-A8RP TCGA-US-A776 TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
        9.40        23.08        27.75        13.81        12.99        11.51 
TCGA-YY-A8LH 
       66.28 

$`LCE2A WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       23.97         2.63        22.22        22.72        22.26        15.91 
TCGA-2J-AABR TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQL TCGA-3A-A9I5 
       14.40         9.11         4.70        22.49         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ 
       23.61         7.36        24.26        28.73        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       12.39        75.12        71.74         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       17.00         5.88        24.07        14.76         4.04         5.03 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8002 
       12.89        13.84        19.50         0.13        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I 
        0.69         3.95        14.93        17.92        21.70        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       41.33        43.79        19.66        21.30        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A9Q5 TCGA-OE-A75W 
        6.02        11.11         7.40         9.44        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 
       15.45        13.68         3.12        21.24        17.26        22.85 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY 
       16.80        14.14         0.39        12.03        13.32        12.76 
TCGA-Z5-AAPL 
        0.69 

  LCE2A MUTATED LCE2A WILD-TYPE 
           1.02            0.13 
  LCE2A MUTATED LCE2A WILD-TYPE 
          66.28           75.12 
  LCE2A MUTATED LCE2A WILD-TYPE 
          12.95           14.14 
[1] "1.0 - 66.3 (12.9)" "0.1 - 75.1 (14.1)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LCE2A MUTATED          1        0         9        30         1        2
  LCE2A WILD-TYPE        3        6        11        69         3        1
D5V3, multiclass
           clus
vv          LCE2A MUTATED LCE2A WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             9              11
  STAGE IIB            30              69
  STAGE III             1               3
  STAGE IV              2               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LCE2A MUTATED    2  3    38
  LCE2A WILD-TYPE  3 10    80
D5V4, multiclass
       clus
vv      LCE2A MUTATED LCE2A WILD-TYPE
  T1                2               3
  T2                3              10
  T3+T4            38              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                 cls
clus               0  1
  LCE2A MUTATED   11 32
  LCE2A WILD-TYPE 21 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     11   32
  LCE2A WILD-TYPE   21   72
   clus
vv  LCE2A MUTATED LCE2A WILD-TYPE
  0            11              21
  1            32              72
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus               0  1
  LCE2A MUTATED   17  2
  LCE2A WILD-TYPE 45  1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     17    2
  LCE2A WILD-TYPE   45    1
   clus
vv  LCE2A MUTATED LCE2A WILD-TYPE
  0            17              45
  1             2               1
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus               0  1
  LCE2A MUTATED   20 23
  LCE2A WILD-TYPE 42 51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     20   23
  LCE2A WILD-TYPE   42   51
        clus
vv       LCE2A MUTATED LCE2A WILD-TYPE
  FEMALE            20              42
  MALE              23              51
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LCE2A MUTATED                                    39
  LCE2A WILD-TYPE                                  83
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LCE2A MUTATED                                       3
  LCE2A WILD-TYPE                                     8
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LCE2A MUTATED                                                  1
  LCE2A WILD-TYPE                                                1
D5V8, multiclass
                                                  clus
vv                                                 LCE2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 LCE2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           83
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
D5V10, continuous
                 vv
clus              R0 R1 R2 RX
  LCE2A MUTATED   26 14  1  1
  LCE2A WILD-TYPE 51 34  0  2
D5V11, multiclass
    clus
vv   LCE2A MUTATED LCE2A WILD-TYPE
  R0            26              51
  R1            14              34
  R2             1               0
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LCE2A MUTATED       1                         3    38
  LCE2A WILD-TYPE     1                         2    87
D5V13, multiclass
                           clus
vv                          LCE2A MUTATED LCE2A WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             3               2
  WHITE                                38              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                 cls
clus               0  1
  LCE2A MUTATED    0 32
  LCE2A WILD-TYPE  3 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED      0   32
  LCE2A WILD-TYPE    3   72
                        clus
vv                       LCE2A MUTATED LCE2A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            32              72
[1] 2 2
[1] FALSE

Clustering(6) Variable = C1QB MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  C1QB MUTATED   11 22
  C1QB WILD-TYPE 51 50
  C1QB MUTATED C1QB WILD-TYPE 
            33            101 
  C1QB MUTATED C1QB WILD-TYPE 
            22             50 
$`C1QB MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABU 
        9.63         2.63        20.61        22.26        15.91         9.11 
TCGA-2J-AABV TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-FB-A4P6 
       21.44        53.00         7.36        34.09        10.13        11.93 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        23.54         4.04         5.03         1.02 
TCGA-H6-A45N TCGA-HZ-7926 TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 
       13.84        17.03        10.85        12.95         4.77        21.90 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7888 TCGA-IB-A6UG TCGA-IB-AAUQ TCGA-OE-A75W 
       19.82        23.80        43.79         1.35         6.02         8.78 
TCGA-Q3-A5QY TCGA-US-A779 TCGA-Z5-AAPL 
       13.68        16.80         0.69 

$`C1QB WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABO 
        2.17        23.97        19.96        22.22        22.72        14.47 
TCGA-2J-AABR TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       14.40         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9J0 
       23.61        20.84        24.26        28.73        15.06        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       75.12        71.74        10.98         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
       17.00         5.88        24.07        14.76        12.43         7.50 
TCGA-FB-AAQ0 TCGA-H6-8124 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       15.55        12.89        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7885 
        5.26         1.08         0.23        49.38        15.35        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04         3.62        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE 
        8.05        12.92        12.46        10.29        19.20        15.45 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        27.75        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        13.32        11.51        12.76        66.28 

  C1QB MUTATED C1QB WILD-TYPE 
          0.69           0.13 
  C1QB MUTATED C1QB WILD-TYPE 
         53.00          75.12 
  C1QB MUTATED C1QB WILD-TYPE 
         12.95          14.14 
[1] "0.7 - 53.0 (12.9)" "0.1 - 75.1 (14.1)"
[1] "hr=" "1.3"
D6V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C1QB MUTATED          2        0         6        24         0        1
  C1QB WILD-TYPE        2        6        14        75         4        2
D6V3, multiclass
           clus
vv          C1QB MUTATED C1QB WILD-TYPE
  STAGE IA             2              2
  STAGE IB             0              6
  STAGE IIA            6             14
  STAGE IIB           24             75
  STAGE III            0              4
  STAGE IV             1              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  C1QB MUTATED    2  2    29
  C1QB WILD-TYPE  3 11    89
D6V4, multiclass
       clus
vv      C1QB MUTATED C1QB WILD-TYPE
  T1               2              3
  T2               2             11
  T3+T4           29             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                cls
clus              0  1
  C1QB MUTATED    8 25
  C1QB WILD-TYPE 24 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED      8   25
  C1QB WILD-TYPE   24   79
   clus
vv  C1QB MUTATED C1QB WILD-TYPE
  0            8             24
  1           25             79
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus              0  1
  C1QB MUTATED   16  1
  C1QB WILD-TYPE 46  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED     16    1
  C1QB WILD-TYPE   46    2
   clus
vv  C1QB MUTATED C1QB WILD-TYPE
  0           16             46
  1            1              2
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus              0  1
  C1QB MUTATED   12 21
  C1QB WILD-TYPE 50 53
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED     12   21
  C1QB WILD-TYPE   50   53
        clus
vv       C1QB MUTATED C1QB WILD-TYPE
  FEMALE           12             50
  MALE             21             53
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C1QB MUTATED                                    30
  C1QB WILD-TYPE                                  92
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C1QB MUTATED                                       3
  C1QB WILD-TYPE                                     8
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C1QB MUTATED                                                  0
  C1QB WILD-TYPE                                                2
D6V8, multiclass
                                                  clus
vv                                                 C1QB MUTATED C1QB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        30             92
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3              8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
D6V10, continuous
                vv
clus             R0 R1 R2 RX
  C1QB MUTATED   17 13  0  1
  C1QB WILD-TYPE 60 35  1  2
D6V11, multiclass
    clus
vv   C1QB MUTATED C1QB WILD-TYPE
  R0           17             60
  R1           13             35
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QB MUTATED       2                         2    29
  C1QB WILD-TYPE     0                         3    96
D6V13, multiclass
                           clus
vv                          C1QB MUTATED C1QB WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               29             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                cls
clus              0  1
  C1QB MUTATED    1 25
  C1QB WILD-TYPE  2 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED      1   25
  C1QB WILD-TYPE    2   79
                        clus
vv                       C1QB MUTATED C1QB WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           25             79
[1] 2 2
[1] FALSE

Clustering(7) Variable = CDKN2A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    9 18
  CDKN2A WILD-TYPE 53 54
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              27              107 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              18               54 
$`CDKN2A MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABK TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 
       20.61        22.72        15.91        22.49        12.95        23.61 
TCGA-3A-A9IB TCGA-3A-A9IU TCGA-3E-AAAY TCGA-F2-6879 TCGA-FB-A545 TCGA-FB-A78T 
        7.36        15.06        75.12        10.98        24.07        12.43 
TCGA-H6-8124 TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A77O 
       12.89        17.03         3.95        21.70         6.38         5.26 
TCGA-IB-7649 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A6UG 
       15.35         4.04        15.81        17.16        15.12         1.35 
TCGA-OE-A75W TCGA-RB-AA9M TCGA-US-A77G 
        8.78         9.40         0.39 

$`CDKN2A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       22.26        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        3.39         9.60        53.00        20.84        24.26        28.73 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H 
       34.09        10.13        12.39        71.74         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-AAPS 
        3.12        17.00         5.88        11.93        14.76         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
        1.02        13.84        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       16.14        10.13        21.60        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
       41.33         3.62        43.79        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       15.98         2.47        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        10.29        19.20        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        3.12        15.32        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       27.75        16.80        14.14        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.39             0.13 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           75.12            71.74 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           15.06            13.68 
[1] "0.4 - 75.1 (15.1)" "0.1 - 71.7 (13.7)"
[1] "hr=" "1.3"
D7V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CDKN2A MUTATED          0        0         1        26         1        0
  CDKN2A WILD-TYPE        4        6        19        73         3        3
D7V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB             26               73
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CDKN2A MUTATED    1  2    25
  CDKN2A WILD-TYPE  4 11    93
D7V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T1                 1                4
  T2                 2               11
  T3+T4             25               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                  cls
clus                0  1
  CDKN2A MUTATED    2 26
  CDKN2A WILD-TYPE 30 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2   26
  CDKN2A WILD-TYPE   30   78
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0              2               30
  1             26               78
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                0  1
  CDKN2A MUTATED   15  0
  CDKN2A WILD-TYPE 47  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     15    0
  CDKN2A WILD-TYPE   47    3
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             15               47
  1              0                3
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                0  1
  CDKN2A MUTATED   11 17
  CDKN2A WILD-TYPE 51 57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11   17
  CDKN2A WILD-TYPE   51   57
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             11               51
  MALE               17               57
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDKN2A MUTATED                                    27
  CDKN2A WILD-TYPE                                  95
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDKN2A MUTATED                                       1
  CDKN2A WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDKN2A MUTATED                                                  0
  CDKN2A WILD-TYPE                                                2
D7V8, multiclass
                                                  clus
vv                                                 CDKN2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CDKN2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, continuous
D7V10, continuous
                  vv
clus               R0 R1 R2 RX
  CDKN2A MUTATED   15 10  0  1
  CDKN2A WILD-TYPE 62 38  1  2
D7V11, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             15               62
  R1             10               38
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       0                         2    25
  CDKN2A WILD-TYPE     2                         3   100
D7V13, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                 25              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                  cls
clus                0  1
  CDKN2A MUTATED    0 20
  CDKN2A WILD-TYPE  3 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   20
  CDKN2A WILD-TYPE    3   84
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             20               84
[1] 2 2
[1] FALSE

Clustering(8) Variable = AEBP1 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  AEBP1 MUTATED   12 13
  AEBP1 WILD-TYPE 50 59
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             25             109 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             13              59 
$`AEBP1 MUTATED`
TCGA-2J-AABE TCGA-2L-AAQI TCGA-3A-A9IB TCGA-F2-A44H TCGA-FB-A4P5 TCGA-H6-A45N 
       22.22         3.39         7.36        19.27         5.88        13.84 
TCGA-HZ-7922 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A77P 
        0.13        12.43        14.93        21.70         6.38        10.85 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7890 
       12.95        49.38         4.77        21.90        19.82        19.66 
TCGA-IB-7891 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-US-A776 TCGA-US-A77G 
       21.30        15.85        15.12        20.88        27.75         0.39 
TCGA-YY-A8LH 
       66.28 

$`AEBP1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
       21.44         4.70        22.49        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       23.61        20.84        24.26        28.73        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        12.39        75.12        71.74        10.98         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00        11.93        24.07        14.76        12.43 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 
        5.03         1.02        12.89        19.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 
       23.21        12.03         0.69         3.95         9.83        17.92 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 
       16.14        10.13        21.60         5.26         1.08         0.23 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       15.81         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        16.80        14.14 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-Z5-AAPL 
        0.69 

  AEBP1 MUTATED AEBP1 WILD-TYPE 
           0.13            0.23 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
          66.28           75.12 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
          15.12           12.99 
[1] "0.1 - 66.3 (15.1)" "0.2 - 75.1 (13.0)"
[1] "hr=" "1.2"
D8V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AEBP1 MUTATED          1        1         4        18         0        1
  AEBP1 WILD-TYPE        3        5        16        81         4        2
D8V3, multiclass
           clus
vv          AEBP1 MUTATED AEBP1 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              1               5
  STAGE IIA             4              16
  STAGE IIB            18              81
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AEBP1 MUTATED    1  2    22
  AEBP1 WILD-TYPE  4 11    96
D8V4, multiclass
       clus
vv      AEBP1 MUTATED AEBP1 WILD-TYPE
  T1                1               4
  T2                2              11
  T3+T4            22              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                 cls
clus               0  1
  AEBP1 MUTATED    6 19
  AEBP1 WILD-TYPE 26 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      6   19
  AEBP1 WILD-TYPE   26   85
   clus
vv  AEBP1 MUTATED AEBP1 WILD-TYPE
  0             6              26
  1            19              85
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus               0  1
  AEBP1 MUTATED   11  1
  AEBP1 WILD-TYPE 51  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED     11    1
  AEBP1 WILD-TYPE   51    2
   clus
vv  AEBP1 MUTATED AEBP1 WILD-TYPE
  0            11              51
  1             1               2
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus               0  1
  AEBP1 MUTATED   13 12
  AEBP1 WILD-TYPE 49 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED     13   12
  AEBP1 WILD-TYPE   49   62
        clus
vv       AEBP1 MUTATED AEBP1 WILD-TYPE
  FEMALE            13              49
  MALE              12              62
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AEBP1 MUTATED                                    21
  AEBP1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AEBP1 MUTATED                                       3
  AEBP1 WILD-TYPE                                     8
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AEBP1 MUTATED                                                  1
  AEBP1 WILD-TYPE                                                1
D8V8, multiclass
                                                  clus
vv                                                 AEBP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 AEBP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
D8V10, continuous
                 vv
clus              R0 R1 R2 RX
  AEBP1 MUTATED   16  8  0  0
  AEBP1 WILD-TYPE 61 40  1  3
D8V11, multiclass
    clus
vv   AEBP1 MUTATED AEBP1 WILD-TYPE
  R0            16              61
  R1             8              40
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AEBP1 MUTATED       0                         0    23
  AEBP1 WILD-TYPE     2                         5   102
D8V13, multiclass
                           clus
vv                          AEBP1 MUTATED AEBP1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                23             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"
D8V14, binary
                 cls
clus               0  1
  AEBP1 MUTATED    0 19
  AEBP1 WILD-TYPE  3 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      0   19
  AEBP1 WILD-TYPE    3   85
                        clus
vv                       AEBP1 MUTATED AEBP1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19              85
[1] 2 2
[1] FALSE

Clustering(9) Variable = RBM47 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2              0  1
  RBM47 MUTATED    9 14
  RBM47 WILD-TYPE 53 58
  RBM47 MUTATED RBM47 WILD-TYPE 
             23             111 
  RBM47 MUTATED RBM47 WILD-TYPE 
             14              58 
$`RBM47 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABR TCGA-2L-AAQI TCGA-3A-A9IU TCGA-FB-A4P6 TCGA-FB-AAPS 
       20.61        14.40         3.39        15.06        11.93         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-HZ-7919 TCGA-HZ-A49H 
       12.53        34.82        15.55         5.03        19.50        16.14 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7888 TCGA-IB-A6UF 
        1.08        12.95        19.82        41.33        43.79        21.90 
TCGA-IB-AAUQ TCGA-LB-A7SX TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-YY-A8LH 
        6.02        12.92        15.32         9.40        66.28 

$`RBM47 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.72        22.26        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
        4.70        22.49        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ 
       20.84         7.36        24.26        28.73        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       12.39        75.12        71.74        10.98         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7922 
       23.54         4.04         1.02        12.89        13.84         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I 
        9.83        12.43        14.93        17.92        21.70        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7645 
        6.38        21.60         5.26        10.85         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A8F3 
       14.17        11.11         7.40         9.44         8.05        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76         0.69 

  RBM47 MUTATED RBM47 WILD-TYPE 
           1.08            0.13 
  RBM47 MUTATED RBM47 WILD-TYPE 
          66.28           75.12 
  RBM47 MUTATED RBM47 WILD-TYPE 
          15.06           13.32 
[1] "1.1 - 66.3 (15.1)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1"  
D9V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM47 MUTATED          0        0         4        20         0        1
  RBM47 WILD-TYPE        4        6        16        79         4        2
D9V3, multiclass
           clus
vv          RBM47 MUTATED RBM47 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             4              16
  STAGE IIB            20              79
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM47 MUTATED    1  2    22
  RBM47 WILD-TYPE  4 11    96
D9V4, multiclass
       clus
vv      RBM47 MUTATED RBM47 WILD-TYPE
  T1                1               4
  T2                2              11
  T3+T4            22              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                 cls
clus               0  1
  RBM47 MUTATED    4 21
  RBM47 WILD-TYPE 28 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      4   21
  RBM47 WILD-TYPE   28   83
   clus
vv  RBM47 MUTATED RBM47 WILD-TYPE
  0             4              28
  1            21              83
[1] 2 2
[1] FALSE
D9V6, binary
                 cls
clus               0  1
  RBM47 MUTATED    8  1
  RBM47 WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      8    1
  RBM47 WILD-TYPE   54    2
   clus
vv  RBM47 MUTATED RBM47 WILD-TYPE
  0             8              54
  1             1               2
[1] 2 2
[1] FALSE
D9V7, binary
                 cls
clus               0  1
  RBM47 MUTATED   16  9
  RBM47 WILD-TYPE 46 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED     16    9
  RBM47 WILD-TYPE   46   65
        clus
vv       RBM47 MUTATED RBM47 WILD-TYPE
  FEMALE            16              46
  MALE               9              65
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM47 MUTATED                                    23
  RBM47 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM47 MUTATED                                       2
  RBM47 WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM47 MUTATED                                                  0
  RBM47 WILD-TYPE                                                2
D9V8, multiclass
                                                  clus
vv                                                 RBM47 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RBM47 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
D9V10, continuous
                 vv
clus              R0 R1 R2 RX
  RBM47 MUTATED   16  8  0  0
  RBM47 WILD-TYPE 61 40  1  3
D9V11, multiclass
    clus
vv   RBM47 MUTATED RBM47 WILD-TYPE
  R0            16              61
  R1             8              40
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM47 MUTATED       1                         2    22
  RBM47 WILD-TYPE     1                         3   103
D9V13, multiclass
                           clus
vv                          RBM47 MUTATED RBM47 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                22             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                 cls
clus               0  1
  RBM47 MUTATED    1 21
  RBM47 WILD-TYPE  2 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      1   21
  RBM47 WILD-TYPE    2   83
                        clus
vv                       RBM47 MUTATED RBM47 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            21              83
[1] 2 2
[1] FALSE

Clustering(10) Variable = ANKRD36 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  ANKRD36 MUTATED   11 12
  ANKRD36 WILD-TYPE 51 60
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               111 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               12                60 
$`ANKRD36 MUTATED`
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABV TCGA-2L-AAQL TCGA-F2-A8YN TCGA-FB-AAQ3 
       22.22        22.72        21.44         9.60        17.00         1.02 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       20.19        23.21         0.69        12.43        14.93        17.92 
TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-AAUN TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-S4-A8RM 
        2.47         7.20         4.73         8.05        10.29        21.24 
TCGA-S4-A8RP TCGA-US-A77E TCGA-XD-AAUG TCGA-YB-A89D TCGA-YY-A8LH 
       23.08        14.14        13.81        11.51        66.28 

$`ANKRD36 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2L-AAQA 
       22.26        15.91        14.47        14.40         9.11         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49         3.39        12.95        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
        7.36        24.26        28.73        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       12.39        75.12        71.74        10.98         7.66        19.27 
TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12         5.88        11.93        24.07        14.76        12.43 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        5.03        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.03         3.95         9.83        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO 
       19.66        21.30         3.85        15.98        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.40         9.44        12.92        12.46        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32         9.40        17.26 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUH TCGA-XD-AAUI 
       22.85        27.75        16.80         0.39        12.99        12.03 
TCGA-XD-AAUL TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.32        12.76         0.69 

  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
             0.69              0.13 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
            66.28             75.12 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
            14.14             13.32 
[1] "0.7 - 66.3 (14.1)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANKRD36 MUTATED          1        2         2        14         2        2
  ANKRD36 WILD-TYPE        3        4        18        85         2        1
D10V3, multiclass
           clus
vv          ANKRD36 MUTATED ANKRD36 WILD-TYPE
  STAGE IA                1                 3
  STAGE IB                2                 4
  STAGE IIA               2                18
  STAGE IIB              14                85
  STAGE III               2                 2
  STAGE IV                2                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ANKRD36 MUTATED    1  2    20
  ANKRD36 WILD-TYPE  4 11    98
D10V4, multiclass
       clus
vv      ANKRD36 MUTATED ANKRD36 WILD-TYPE
  T1                  1                 4
  T2                  2                11
  T3+T4              20                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    7 16
  ANKRD36 WILD-TYPE 25 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      7   16
  ANKRD36 WILD-TYPE   25   88
   clus
vv  ANKRD36 MUTATED ANKRD36 WILD-TYPE
  0               7                25
  1              16                88
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    8  2
  ANKRD36 WILD-TYPE 54  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      8    2
  ANKRD36 WILD-TYPE   54    1
   clus
vv  ANKRD36 MUTATED ANKRD36 WILD-TYPE
  0               8                54
  1               2                 1
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED   11 12
  ANKRD36 WILD-TYPE 51 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED     11   12
  ANKRD36 WILD-TYPE   51   62
        clus
vv       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  FEMALE              11                51
  MALE                12                62
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD36 MUTATED                                    21
  ANKRD36 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD36 MUTATED                                       2
  ANKRD36 WILD-TYPE                                     9
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD36 MUTATED                                                  0
  ANKRD36 WILD-TYPE                                                2
D10V8, multiclass
                                                  clus
vv                                                 ANKRD36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ANKRD36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
D10V10, continuous
                   vv
clus                R0 R1 R2 RX
  ANKRD36 MUTATED   14  8  0  1
  ANKRD36 WILD-TYPE 63 40  1  2
D10V11, multiclass
    clus
vv   ANKRD36 MUTATED ANKRD36 WILD-TYPE
  R0              14                63
  R1               8                40
  R2               0                 1
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD36 MUTATED       0                         0    23
  ANKRD36 WILD-TYPE     2                         5   102
D10V13, multiclass
                           clus
vv                          ANKRD36 MUTATED ANKRD36 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  23               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"
D10V14, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    0 18
  ANKRD36 WILD-TYPE  3 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      0   18
  ANKRD36 WILD-TYPE    3   86
                        clus
vv                       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              18                86
[1] 2 2
[1] FALSE

Clustering(11) Variable = RFX1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  RFX1 MUTATED    9 14
  RFX1 WILD-TYPE 53 58
  RFX1 MUTATED RFX1 WILD-TYPE 
            23            111 
  RFX1 MUTATED RFX1 WILD-TYPE 
            14             58 
$`RFX1 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABK TCGA-2L-AAQI TCGA-3A-A9I9 
        2.17        23.97         2.63        15.91         3.39        20.84 
TCGA-F2-A44G TCGA-FB-A545 TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-HZ-A49G TCGA-HZ-A77O 
        7.66        24.07        15.55         1.02        21.70         5.26 
TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-8126 
        4.77        15.35        19.82         3.62        43.79         2.47 
TCGA-IB-A6UF TCGA-IB-AAUO TCGA-IB-AAUP TCGA-M8-A5N4 TCGA-Z5-AAPL 
       21.90         7.86        14.17        19.20         0.69 

$`RFX1 WILD-TYPE`
TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH 
        9.63        20.61        19.96        22.22        22.72        22.26 
TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        14.40         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        53.00        23.61         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74        10.98        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 
       23.54         4.04         5.03        12.89        13.84        19.50 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49H 
        3.95         9.83        12.43        14.93        17.92        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       10.13         6.38        21.60        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       12.95        49.38        21.90        23.80        41.33         4.04 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 
       15.81        19.66        21.30         3.85        15.98        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
       12.00        15.85         7.20        15.12        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUR 
        8.22        15.88         0.26         4.73         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  RFX1 MUTATED RFX1 WILD-TYPE 
          0.69           0.13 
  RFX1 MUTATED RFX1 WILD-TYPE 
         43.79          75.12 
  RFX1 MUTATED RFX1 WILD-TYPE 
         14.17          13.68 
[1] "0.7 - 43.8 (14.2)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D11V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RFX1 MUTATED          0        0         5        17         1        0
  RFX1 WILD-TYPE        4        6        15        82         3        3
D11V3, multiclass
           clus
vv          RFX1 MUTATED RFX1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            5             15
  STAGE IIB           17             82
  STAGE III            1              3
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RFX1 MUTATED    0  3    20
  RFX1 WILD-TYPE  5 10    98
D11V4, multiclass
       clus
vv      RFX1 MUTATED RFX1 WILD-TYPE
  T1               0              5
  T2               3             10
  T3+T4           20             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                cls
clus              0  1
  RFX1 MUTATED    5 18
  RFX1 WILD-TYPE 27 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      5   18
  RFX1 WILD-TYPE   27   86
   clus
vv  RFX1 MUTATED RFX1 WILD-TYPE
  0            5             27
  1           18             86
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus              0  1
  RFX1 MUTATED   17  0
  RFX1 WILD-TYPE 45  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED     17    0
  RFX1 WILD-TYPE   45    3
   clus
vv  RFX1 MUTATED RFX1 WILD-TYPE
  0           17             45
  1            0              3
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus              0  1
  RFX1 MUTATED   13 10
  RFX1 WILD-TYPE 49 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED     13   10
  RFX1 WILD-TYPE   49   64
        clus
vv       RFX1 MUTATED RFX1 WILD-TYPE
  FEMALE           13             49
  MALE             10             64
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RFX1 MUTATED                                    21
  RFX1 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RFX1 MUTATED                                       2
  RFX1 WILD-TYPE                                     9
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RFX1 MUTATED                                                  0
  RFX1 WILD-TYPE                                                2
D11V8, multiclass
                                                  clus
vv                                                 RFX1 MUTATED RFX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        21            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, continuous
D11V10, continuous
                vv
clus             R0 R1 R2 RX
  RFX1 MUTATED    9 13  0  0
  RFX1 WILD-TYPE 68 35  1  3
D11V11, multiclass
    clus
vv   RFX1 MUTATED RFX1 WILD-TYPE
  R0            9             68
  R1           13             35
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RFX1 MUTATED       0                         1    20
  RFX1 WILD-TYPE     2                         4   105
D11V13, multiclass
                           clus
vv                          RFX1 MUTATED RFX1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               20            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                cls
clus              0  1
  RFX1 MUTATED    0 16
  RFX1 WILD-TYPE  3 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      0   16
  RFX1 WILD-TYPE    3   88
                        clus
vv                       RFX1 MUTATED RFX1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           16             88
[1] 2 2
[1] FALSE

Clustering(12) Variable = TYRO3 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  TYRO3 MUTATED    6  7
  TYRO3 WILD-TYPE 56 65
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             13             121 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              7              65 
$`TYRO3 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9IX TCGA-FB-A4P6 TCGA-FB-A78T 
       23.97         9.11        22.49        34.09        11.93        12.43 
TCGA-FB-AAQ1 TCGA-HZ-A49G TCGA-IB-7644 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-OE-A75W 
        4.04        21.70        12.95        12.00        20.88         8.78 
TCGA-US-A779 
       16.80 

$`TYRO3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABV 
       22.72        22.26        15.91        14.47        14.40        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ 
       20.84         7.36        24.26        28.73        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       12.39        75.12        71.74        10.98         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS 
        3.12        17.00         5.88        24.07        14.76         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        23.54        15.55         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        17.16        15.85         7.20        15.12 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE 
        8.05        12.92        12.46        10.29        19.20        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       23.08        22.85        27.75        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  TYRO3 MUTATED TYRO3 WILD-TYPE 
           4.04            0.13 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          34.09           75.12 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          12.95           13.81 
[1] "4.0 - 34.1 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.1"
D12V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TYRO3 MUTATED          1        0         1        10         0        1
  TYRO3 WILD-TYPE        3        6        19        89         4        2
D12V3, multiclass
           clus
vv          TYRO3 MUTATED TYRO3 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB            10              89
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TYRO3 MUTATED     1   2    10
  TYRO3 WILD-TYPE   4  11   108
D12V4, multiclass
       clus
vv      TYRO3 MUTATED TYRO3 WILD-TYPE
  T1                1               4
  T2                2              11
  T3+T4            10             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                 cls
clus               0  1
  TYRO3 MUTATED    2 11
  TYRO3 WILD-TYPE 30 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      2   11
  TYRO3 WILD-TYPE   30   93
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0             2              30
  1            11              93
[1] 2 2
[1] FALSE
D12V6, binary
                 cls
clus               0  1
  TYRO3 MUTATED    7  1
  TYRO3 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      7    1
  TYRO3 WILD-TYPE   55    2
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0             7              55
  1             1               2
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus               0  1
  TYRO3 MUTATED    5  8
  TYRO3 WILD-TYPE 57 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      5    8
  TYRO3 WILD-TYPE   57   66
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  FEMALE             5              57
  MALE               8              66
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TYRO3 MUTATED                                    12
  TYRO3 WILD-TYPE                                 110
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TYRO3 MUTATED                                       1
  TYRO3 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TYRO3 MUTATED                                                  0
  TYRO3 WILD-TYPE                                                2
D12V8, multiclass
                                                  clus
vv                                                 TYRO3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TYRO3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, continuous
D12V10, continuous
                 vv
clus              R0 R1 R2 RX
  TYRO3 MUTATED    9  3  0  0
  TYRO3 WILD-TYPE 68 45  1  3
D12V11, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  R0             9              68
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TYRO3 MUTATED       0                         0    13
  TYRO3 WILD-TYPE     2                         5   112
D12V13, multiclass
                           clus
vv                          TYRO3 MUTATED TYRO3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                13             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                 cls
clus               0  1
  TYRO3 MUTATED    0  9
  TYRO3 WILD-TYPE  3 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      0    9
  TYRO3 WILD-TYPE    3   95
                        clus
vv                       TYRO3 MUTATED TYRO3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9              95
[1] 2 2
[1] FALSE

Clustering(13) Variable = SMAD4 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED   12 15
  SMAD4 WILD-TYPE 50 57
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             27             107 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             15              57 
$`SMAD4 MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3E-AAAZ 
        2.63        19.96        22.22        28.73        34.09        71.74 
TCGA-FB-A78T TCGA-FB-AAPY TCGA-FB-AAQ3 TCGA-HZ-7919 TCGA-HZ-8315 TCGA-HZ-8317 
       12.43        34.82         1.02        19.50         9.83        12.43 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7891 
        1.08        12.95        19.82         4.04        15.81        21.30 
TCGA-IB-A5SP TCGA-IB-AAUM TCGA-IB-AAUR TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-S4-A8RM 
       15.85         0.26        11.11        10.29        15.45        21.24 
TCGA-S4-A8RP TCGA-US-A77G TCGA-YB-A89D 
       23.08         0.39        11.51 

$`SMAD4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH 
        2.17        23.97         9.63        20.61        22.72        22.26 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 
       20.84         7.36        24.26        15.06        10.13        12.39 
TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       75.12        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        11.93        24.07        14.76         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03        12.89        13.84 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
        3.95        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7645 
        6.38        21.60         5.26        10.85         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 
        4.77        21.90        15.35        23.80        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       43.79        19.66         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         4.73         7.86        14.17         6.02 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        7.40         9.44         8.05        12.92        12.46        19.20 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO 
        8.78        13.68         3.12        15.32         9.40        17.26 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        27.75        16.80        14.14        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        12.76        66.28         0.69 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.26            0.13 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          71.74           75.12 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          15.45           13.68 
[1] "0.3 - 71.7 (15.4)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D13V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SMAD4 MUTATED          2        0         4        21         0        1
  SMAD4 WILD-TYPE        2        6        16        78         4        2
D13V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE IA              2               2
  STAGE IB              0               6
  STAGE IIA             4              16
  STAGE IIB            21              78
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SMAD4 MUTATED    2  2    24
  SMAD4 WILD-TYPE  3 11    94
D13V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                2               3
  T2                2              11
  T3+T4            24              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                 cls
clus               0  1
  SMAD4 MUTATED    6 22
  SMAD4 WILD-TYPE 26 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      6   22
  SMAD4 WILD-TYPE   26   82
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             6              26
  1            22              82
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus               0  1
  SMAD4 MUTATED   12  1
  SMAD4 WILD-TYPE 50  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     12    1
  SMAD4 WILD-TYPE   50    2
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            12              50
  1             1               2
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED   14 14
  SMAD4 WILD-TYPE 48 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     14   14
  SMAD4 WILD-TYPE   48   60
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            14              48
  MALE              14              60
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMAD4 MUTATED                                    27
  SMAD4 WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMAD4 MUTATED                                       1
  SMAD4 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMAD4 MUTATED                                                  0
  SMAD4 WILD-TYPE                                                2
D13V8, multiclass
                                                  clus
vv                                                 SMAD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SMAD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, continuous
D13V10, continuous
                 vv
clus              R0 R1 R2 RX
  SMAD4 MUTATED   17  9  0  0
  SMAD4 WILD-TYPE 60 39  1  3
D13V11, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            17              60
  R1             9              39
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       0                         0    28
  SMAD4 WILD-TYPE     2                         5    97
D13V13, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                28              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1 22
  SMAD4 WILD-TYPE  2 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1   22
  SMAD4 WILD-TYPE    2   82
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            22              82
[1] 2 2
[1] FALSE

Clustering(14) Variable = GPR6 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  GPR6 MUTATED    5  6
  GPR6 WILD-TYPE 57 66
  GPR6 MUTATED GPR6 WILD-TYPE 
            11            123 
  GPR6 MUTATED GPR6 WILD-TYPE 
             6             66 
$`GPR6 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABR TCGA-F2-6879 TCGA-HZ-A49G TCGA-IB-7651 TCGA-IB-7652 
        2.17        14.40        10.98        21.70        19.82        23.80 
TCGA-IB-AAUP TCGA-OE-A75W TCGA-S4-A8RP TCGA-US-A774 TCGA-Z5-AAPL 
       14.17         8.78        23.08        22.85         0.69 

$`GPR6 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.72        22.26        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A44G 
       34.09        10.13        12.39        75.12        71.74         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.35        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-US-A779 
       15.32         9.40        21.24        17.26        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  GPR6 MUTATED GPR6 WILD-TYPE 
          0.69           0.13 
  GPR6 MUTATED GPR6 WILD-TYPE 
         23.80          75.12 
  GPR6 MUTATED GPR6 WILD-TYPE 
         14.40          13.32 
[1] "0.7 - 23.8 (14.4)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.1"
D14V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPR6 MUTATED          0        0         3         9         0        0
  GPR6 WILD-TYPE        4        6        17        90         4        3
D14V3, multiclass
           clus
vv          GPR6 MUTATED GPR6 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            3             17
  STAGE IIB            9             90
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  GPR6 MUTATED     0   1    11
  GPR6 WILD-TYPE   5  12   107
D14V4, multiclass
       clus
vv      GPR6 MUTATED GPR6 WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4           11            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                cls
clus              0  1
  GPR6 MUTATED    3  9
  GPR6 WILD-TYPE 29 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      3    9
  GPR6 WILD-TYPE   29   95
   clus
vv  GPR6 MUTATED GPR6 WILD-TYPE
  0            3             29
  1            9             95
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus              0  1
  GPR6 MUTATED    8  0
  GPR6 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      8    0
  GPR6 WILD-TYPE   54    3
   clus
vv  GPR6 MUTATED GPR6 WILD-TYPE
  0            8             54
  1            0              3
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus              0  1
  GPR6 MUTATED    8  4
  GPR6 WILD-TYPE 54 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      8    4
  GPR6 WILD-TYPE   54   70
        clus
vv       GPR6 MUTATED GPR6 WILD-TYPE
  FEMALE            8             54
  MALE              4             70
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR6 MUTATED                                    10
  GPR6 WILD-TYPE                                 112
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR6 MUTATED                                       2
  GPR6 WILD-TYPE                                     9
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR6 MUTATED                                                  0
  GPR6 WILD-TYPE                                                2
D14V8, multiclass
                                                  clus
vv                                                 GPR6 MUTATED GPR6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        10            112
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, continuous
D14V10, continuous
                vv
clus             R0 R1 R2 RX
  GPR6 MUTATED    9  3  0  0
  GPR6 WILD-TYPE 68 45  1  3
D14V11, multiclass
    clus
vv   GPR6 MUTATED GPR6 WILD-TYPE
  R0            9             68
  R1            3             45
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR6 MUTATED       1                         0    11
  GPR6 WILD-TYPE     1                         5   114
D14V13, multiclass
                           clus
vv                          GPR6 MUTATED GPR6 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               11            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                cls
clus              0  1
  GPR6 MUTATED    1  7
  GPR6 WILD-TYPE  2 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      1    7
  GPR6 WILD-TYPE    2   97
                        clus
vv                       GPR6 MUTATED GPR6 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            7             97
[1] 2 2
[1] FALSE

Clustering(15) Variable = LZTS1 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  LZTS1 MUTATED    2  6
  LZTS1 WILD-TYPE 60 66
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              8             126 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              6              66 
$`LZTS1 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABO TCGA-HZ-7926 TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-IB-7651 
       20.61        14.47        17.03        10.13         6.38        19.82 
TCGA-IB-7893 TCGA-IB-7897 
        3.85        15.98 

$`LZTS1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.72        22.26        15.91        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
       13.84        19.50         0.13        20.19        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       21.70        16.14        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.66        21.30         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  LZTS1 MUTATED LZTS1 WILD-TYPE 
           3.85            0.13 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
          20.61           75.12 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
         15.225          13.500 
[1] "3.9 - 20.6 (15.2)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.7"
D15V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LZTS1 MUTATED          0        0         1         7         0        0
  LZTS1 WILD-TYPE        4        6        19        92         4        3
D15V3, multiclass
           clus
vv          LZTS1 MUTATED LZTS1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             7              92
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  LZTS1 MUTATED     0   0     8
  LZTS1 WILD-TYPE   5  13   110
D15V4, multiclass
       clus
vv      LZTS1 MUTATED LZTS1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             8             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                 cls
clus               0  1
  LZTS1 MUTATED    1  7
  LZTS1 WILD-TYPE 31 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      1    7
  LZTS1 WILD-TYPE   31   97
   clus
vv  LZTS1 MUTATED LZTS1 WILD-TYPE
  0             1              31
  1             7              97
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus               0  1
  LZTS1 MUTATED    5  0
  LZTS1 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      5    0
  LZTS1 WILD-TYPE   57    3
   clus
vv  LZTS1 MUTATED LZTS1 WILD-TYPE
  0             5              57
  1             0               3
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  LZTS1 MUTATED    3  5
  LZTS1 WILD-TYPE 59 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      3    5
  LZTS1 WILD-TYPE   59   69
        clus
vv       LZTS1 MUTATED LZTS1 WILD-TYPE
  FEMALE             3              59
  MALE               5              69
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LZTS1 MUTATED                                     8
  LZTS1 WILD-TYPE                                 114
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LZTS1 MUTATED                                       0
  LZTS1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LZTS1 MUTATED                                                  0
  LZTS1 WILD-TYPE                                                2
D15V8, multiclass
                                                  clus
vv                                                 LZTS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 LZTS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          114
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, continuous
[1] "Remove cluster labels:" "LZTS1 MUTATED"         
clus
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
D15V10, continuous
[1] "Remove cluster labels:" "LZTS1 MUTATED"         
clus
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-3A-A9IB 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-YY-A8LH 
"LZTS1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  LZTS1 MUTATED    5  2  0  1
  LZTS1 WILD-TYPE 72 46  1  2
D15V11, multiclass
    clus
vv   LZTS1 MUTATED LZTS1 WILD-TYPE
  R0             5              72
  R1             2              46
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LZTS1 MUTATED       0                         1     7
  LZTS1 WILD-TYPE     2                         4   118
D15V13, multiclass
                           clus
vv                          LZTS1 MUTATED LZTS1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                 cls
clus               0  1
  LZTS1 MUTATED    0  5
  LZTS1 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      0    5
  LZTS1 WILD-TYPE    3   99
                        clus
vv                       LZTS1 MUTATED LZTS1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(16) Variable = NCOA3 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2              0  1
  NCOA3 MUTATED    5  8
  NCOA3 WILD-TYPE 57 64
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             13             121 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              8              64 
$`NCOA3 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABK TCGA-3E-AAAZ TCGA-F2-A8YN TCGA-FB-AAQ1 TCGA-HZ-7919 
        9.63        15.91        71.74        17.00         4.04        19.50 
TCGA-HZ-8317 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-M8-A5N4 
       12.43        15.35        19.82         1.35        12.46        19.20 
TCGA-S4-A8RO 
       17.26 

$`NCOA3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.72        22.26        14.47        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-A44G 
       34.09        10.13        12.39        75.12        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12         5.88        11.93        24.07        14.76 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.43         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7922 TCGA-HZ-7925 
        5.03         1.02        12.89        13.84         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       49.38         4.77        21.90        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE 
        9.44         8.05        12.92        10.29         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RP 
       13.68         3.12        15.32         9.40        21.24        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  NCOA3 MUTATED NCOA3 WILD-TYPE 
           1.35            0.13 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          71.74           75.12 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          15.91           13.32 
[1] "1.4 - 71.7 (15.9)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.1"
D16V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NCOA3 MUTATED          0        0         5         8         0        0
  NCOA3 WILD-TYPE        4        6        15        91         4        3
D16V3, multiclass
           clus
vv          NCOA3 MUTATED NCOA3 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             5              15
  STAGE IIB             8              91
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NCOA3 MUTATED     0   0    13
  NCOA3 WILD-TYPE   5  13   105
D16V4, multiclass
       clus
vv      NCOA3 MUTATED NCOA3 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4            13             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                 cls
clus               0  1
  NCOA3 MUTATED    5  8
  NCOA3 WILD-TYPE 27 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      5    8
  NCOA3 WILD-TYPE   27   96
   clus
vv  NCOA3 MUTATED NCOA3 WILD-TYPE
  0             5              27
  1             8              96
[1] 2 2
[1] FALSE
D16V6, binary
                 cls
clus               0  1
  NCOA3 MUTATED    8  0
  NCOA3 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      8    0
  NCOA3 WILD-TYPE   54    3
   clus
vv  NCOA3 MUTATED NCOA3 WILD-TYPE
  0             8              54
  1             0               3
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus               0  1
  NCOA3 MUTATED    7  6
  NCOA3 WILD-TYPE 55 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      7    6
  NCOA3 WILD-TYPE   55   68
        clus
vv       NCOA3 MUTATED NCOA3 WILD-TYPE
  FEMALE             7              55
  MALE               6              68
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NCOA3 MUTATED                                    13
  NCOA3 WILD-TYPE                                 109
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NCOA3 MUTATED                                       0
  NCOA3 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NCOA3 MUTATED                                                  0
  NCOA3 WILD-TYPE                                                2
D16V8, multiclass
                                                  clus
vv                                                 NCOA3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NCOA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          109
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, continuous
D16V10, continuous
                 vv
clus              R0 R1 R2 RX
  NCOA3 MUTATED    3  9  0  0
  NCOA3 WILD-TYPE 74 39  1  3
D16V11, multiclass
    clus
vv   NCOA3 MUTATED NCOA3 WILD-TYPE
  R0             3              74
  R1             9              39
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NCOA3 MUTATED       0                         1    10
  NCOA3 WILD-TYPE     2                         4   115
D16V13, multiclass
                           clus
vv                          NCOA3 MUTATED NCOA3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                10             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                 cls
clus               0  1
  NCOA3 MUTATED    1  8
  NCOA3 WILD-TYPE  2 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      1    8
  NCOA3 WILD-TYPE    2   96
                        clus
vv                       NCOA3 MUTATED NCOA3 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             8              96
[1] 2 2
[1] FALSE

Clustering(17) Variable = SIK3 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  SIK3 MUTATED    5  7
  SIK3 WILD-TYPE 57 65
  SIK3 MUTATED SIK3 WILD-TYPE 
            12            122 
  SIK3 MUTATED SIK3 WILD-TYPE 
             7             65 
$`SIK3 MUTATED`
TCGA-2J-AABU TCGA-FB-A4P6 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-IB-7649 TCGA-IB-7888 
        9.11        11.93        17.03        12.03        15.35        43.79 
TCGA-IB-7890 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-US-A774 
       19.66        15.85        21.90        12.46        13.68        22.85 

$`SIK3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 
       13.84        19.50         0.13        20.19        23.21         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 
       19.82        23.80        41.33         4.04         3.62        15.81 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        15.12        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.40         9.44         8.05        12.92        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
        8.78        15.45         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  SIK3 MUTATED SIK3 WILD-TYPE 
          9.11           0.13 
  SIK3 MUTATED SIK3 WILD-TYPE 
         43.79          75.12 
  SIK3 MUTATED SIK3 WILD-TYPE 
        15.600         13.155 
[1] "9.1 - 43.8 (15.6)" "0.1 - 75.1 (13.2)"
[1] "hr=" "1.1"
D17V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SIK3 MUTATED          0        1         3         8         0        0
  SIK3 WILD-TYPE        4        5        17        91         4        3
D17V3, multiclass
           clus
vv          SIK3 MUTATED SIK3 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             1              5
  STAGE IIA            3             17
  STAGE IIB            8             91
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  SIK3 MUTATED     0   1    11
  SIK3 WILD-TYPE   5  12   107
D17V4, multiclass
       clus
vv      SIK3 MUTATED SIK3 WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4           11            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                cls
clus              0  1
  SIK3 MUTATED    4  8
  SIK3 WILD-TYPE 28 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      4    8
  SIK3 WILD-TYPE   28   96
   clus
vv  SIK3 MUTATED SIK3 WILD-TYPE
  0            4             28
  1            8             96
[1] 2 2
[1] FALSE
D17V6, binary
                cls
clus              0  1
  SIK3 MUTATED    6  0
  SIK3 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      6    0
  SIK3 WILD-TYPE   56    3
   clus
vv  SIK3 MUTATED SIK3 WILD-TYPE
  0            6             56
  1            0              3
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus              0  1
  SIK3 MUTATED    4  8
  SIK3 WILD-TYPE 58 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      4    8
  SIK3 WILD-TYPE   58   66
        clus
vv       SIK3 MUTATED SIK3 WILD-TYPE
  FEMALE            4             58
  MALE              8             66
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIK3 MUTATED                                    12
  SIK3 WILD-TYPE                                 110
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIK3 MUTATED                                       0
  SIK3 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIK3 MUTATED                                                  0
  SIK3 WILD-TYPE                                                2
D17V8, multiclass
                                                  clus
vv                                                 SIK3 MUTATED SIK3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        12            110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, continuous
D17V10, continuous
                vv
clus             R0 R1 R2 RX
  SIK3 MUTATED    7  3  0  1
  SIK3 WILD-TYPE 70 45  1  2
D17V11, multiclass
    clus
vv   SIK3 MUTATED SIK3 WILD-TYPE
  R0            7             70
  R1            3             45
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIK3 MUTATED       0                         3     7
  SIK3 WILD-TYPE     2                         2   118
D17V13, multiclass
                           clus
vv                          SIK3 MUTATED SIK3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            3              2
  WHITE                                7            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                cls
clus              0  1
  SIK3 MUTATED    0  8
  SIK3 WILD-TYPE  3 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      0    8
  SIK3 WILD-TYPE    3   96
                        clus
vv                       SIK3 MUTATED SIK3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8             96
[1] 2 2
[1] FALSE

Clustering(18) Variable = ZMIZ2 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  ZMIZ2 MUTATED    4  8
  ZMIZ2 WILD-TYPE 58 64
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             122 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              8              64 
$`ZMIZ2 MUTATED`
TCGA-2J-AABH TCGA-F2-A44G TCGA-FB-A545 TCGA-HZ-8519 TCGA-IB-7644 TCGA-IB-7651 
       22.26         7.66        24.07        14.93        12.95        19.82 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-US-A779 TCGA-US-A77G 
        4.04        17.16        15.12        20.88        16.80         0.39 

$`ZMIZ2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.22        22.72        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8636 TCGA-HZ-A49G 
        0.69         3.95         9.83        12.43        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        1.08         0.23        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       21.30         3.85        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        27.75        14.14 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
           0.39            0.13 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
          24.07           75.12 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
         15.960          13.155 
[1] "0.4 - 24.1 (16.0)" "0.1 - 75.1 (13.2)"
[1] "hr=" "1.3"
D18V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZMIZ2 MUTATED          1        0         1         9         0        1
  ZMIZ2 WILD-TYPE        3        6        19        90         4        2
D18V3, multiclass
           clus
vv          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             9              90
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ZMIZ2 MUTATED     1   0    11
  ZMIZ2 WILD-TYPE   4  13   107
D18V4, multiclass
       clus
vv      ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4            11             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    2 10
  ZMIZ2 WILD-TYPE 30 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      2   10
  ZMIZ2 WILD-TYPE   30   94
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             2              30
  1            10              94
[1] 2 2
[1] FALSE
D18V6, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    8  1
  ZMIZ2 WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      8    1
  ZMIZ2 WILD-TYPE   54    2
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             8              54
  1             1               2
[1] 2 2
[1] FALSE
D18V7, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    7  5
  ZMIZ2 WILD-TYPE 55 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      7    5
  ZMIZ2 WILD-TYPE   55   69
        clus
vv       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  FEMALE             7              55
  MALE               5              69
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMIZ2 MUTATED                                    10
  ZMIZ2 WILD-TYPE                                 112
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMIZ2 MUTATED                                       2
  ZMIZ2 WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMIZ2 MUTATED                                                  0
  ZMIZ2 WILD-TYPE                                                2
D18V8, multiclass
                                                  clus
vv                                                 ZMIZ2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZMIZ2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          112
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, continuous
D18V10, continuous
                 vv
clus              R0 R1 R2 RX
  ZMIZ2 MUTATED    7  4  0  0
  ZMIZ2 WILD-TYPE 70 44  1  3
D18V11, multiclass
    clus
vv   ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  R0             7              70
  R1             4              44
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ2 MUTATED       0                         0    12
  ZMIZ2 WILD-TYPE     2                         5   113
D18V13, multiclass
                           clus
vv                          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                12             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    0 11
  ZMIZ2 WILD-TYPE  3 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      0   11
  ZMIZ2 WILD-TYPE    3   93
                        clus
vv                       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11              93
[1] 2 2
[1] FALSE

Clustering(19) Variable = IRS4 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2             0  1
  IRS4 MUTATED    9  4
  IRS4 WILD-TYPE 53 68
  IRS4 MUTATED IRS4 WILD-TYPE 
            13            121 
  IRS4 MUTATED IRS4 WILD-TYPE 
             4             68 
$`IRS4 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABU TCGA-F2-A8YN TCGA-FB-AAPS TCGA-HZ-A49G TCGA-HZ-A49H 
       23.97         9.11        17.00         7.50        21.70        16.14 
TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7887 TCGA-IB-AAUM TCGA-S4-A8RO 
        4.77        19.82        23.80         3.62         0.26        17.26 
TCGA-Z5-AAPL 
        0.69 

$`IRS4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABV 
       22.72        22.26        15.91        14.47        14.40        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
        7.66        19.27         3.12         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       14.76        12.43        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 
        4.04         5.03         1.02        12.89        13.84        19.50 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49I 
        3.95         9.83        12.43        14.93        17.92        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 
       12.95        49.38        21.90        15.35        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22        15.88         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  IRS4 MUTATED IRS4 WILD-TYPE 
          0.26           0.13 
  IRS4 MUTATED IRS4 WILD-TYPE 
         23.97          75.12 
  IRS4 MUTATED IRS4 WILD-TYPE 
         16.14          13.68 
[1] "0.3 - 24.0 (16.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.6"
D19V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IRS4 MUTATED          0        0         2        12         0        0
  IRS4 WILD-TYPE        4        6        18        87         4        3
D19V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            2             18
  STAGE IIB           12             87
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  IRS4 MUTATED     0   4    10
  IRS4 WILD-TYPE   5   9   108
D19V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T1               0              5
  T2               4              9
  T3+T4           10            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                cls
clus              0  1
  IRS4 MUTATED    2 12
  IRS4 WILD-TYPE 30 92
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2   12
  IRS4 WILD-TYPE   30   92
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            2             30
  1           12             92
[1] 2 2
[1] FALSE
D19V6, binary
                cls
clus              0  1
  IRS4 MUTATED    9  0
  IRS4 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      9    0
  IRS4 WILD-TYPE   53    3
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            9             53
  1            0              3
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus              0  1
  IRS4 MUTATED    9  5
  IRS4 WILD-TYPE 53 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      9    5
  IRS4 WILD-TYPE   53   69
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            9             53
  MALE              5             69
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS4 MUTATED                                    13
  IRS4 WILD-TYPE                                 109
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS4 MUTATED                                       1
  IRS4 WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS4 MUTATED                                                  0
  IRS4 WILD-TYPE                                                2
D19V8, multiclass
                                                  clus
vv                                                 IRS4 MUTATED IRS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        13            109
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, continuous
D19V10, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPY     TCGA-H6-8124 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-YY-A8LH 
"IRS4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  IRS4 MUTATED    8  6  0  0
  IRS4 WILD-TYPE 69 42  1  3
D19V11, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0            8             69
  R1            6             42
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED       1                         0    13
  IRS4 WILD-TYPE     1                         5   112
D19V13, multiclass
                           clus
vv                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               13            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                cls
clus              0  1
  IRS4 MUTATED    1 11
  IRS4 WILD-TYPE  2 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1   11
  IRS4 WILD-TYPE    2   93
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           11             93
[1] 2 2
[1] FALSE

Clustering(20) Variable = ESPN MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  ESPN MUTATED    3  2
  ESPN WILD-TYPE 59 70
  ESPN MUTATED ESPN WILD-TYPE 
             5            129 
  ESPN MUTATED ESPN WILD-TYPE 
             2             70 
$`ESPN MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IX TCGA-IB-AAUR TCGA-YB-A89D 
       20.84        24.26        34.09        11.11        11.51 

$`ESPN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU 
        9.60        53.00        23.61         7.36        28.73        15.06 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        12.39        75.12        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17         6.02         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  ESPN MUTATED ESPN WILD-TYPE 
         11.11           0.13 
  ESPN MUTATED ESPN WILD-TYPE 
         34.09          75.12 
  ESPN MUTATED ESPN WILD-TYPE 
         20.84          13.68 
[1] "11.1 - 34.1 (20.8)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "2.1"
D20V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ESPN MUTATED          1        0         1         3         0        0
  ESPN WILD-TYPE        3        6        19        96         4        3
D20V3, multiclass
           clus
vv          ESPN MUTATED ESPN WILD-TYPE
  STAGE IA             1              3
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  ESPN MUTATED     1   0     4
  ESPN WILD-TYPE   4  13   114
D20V4, multiclass
       clus
vv      ESPN MUTATED ESPN WILD-TYPE
  T1               1              4
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                cls
clus               0   1
  ESPN MUTATED     2   3
  ESPN WILD-TYPE  30 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      2    3
  ESPN WILD-TYPE   30  101
   clus
vv  ESPN MUTATED ESPN WILD-TYPE
  0            2             30
  1            3            101
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus              0  1
  ESPN MUTATED    1  0
  ESPN WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      1    0
  ESPN WILD-TYPE   61    3
   clus
vv  ESPN MUTATED ESPN WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus              0  1
  ESPN MUTATED    1  4
  ESPN WILD-TYPE 61 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      1    4
  ESPN WILD-TYPE   61   70
        clus
vv       ESPN MUTATED ESPN WILD-TYPE
  FEMALE            1             61
  MALE              4             70
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ESPN MUTATED                                     5
  ESPN WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ESPN MUTATED                                       0
  ESPN WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ESPN MUTATED                                                  0
  ESPN WILD-TYPE                                                2
D20V8, multiclass
                                                  clus
vv                                                 ESPN MUTATED ESPN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, continuous
[1] "Remove cluster labels:" "ESPN MUTATED"          
clus
  ESPN MUTATED ESPN WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-F2-A8YN     TCGA-FB-A4P5     TCGA-FB-A4P6 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-H6-8124     TCGA-H6-A45N     TCGA-HZ-A77Q     TCGA-HZ-A8P0 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7651 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7891 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" 
D20V10, continuous
[1] "Remove cluster labels:" "ESPN MUTATED"          
clus
  ESPN MUTATED ESPN WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ESPN MUTATED    4  1  0  0
  ESPN WILD-TYPE 73 47  1  3
D20V11, multiclass
    clus
vv   ESPN MUTATED ESPN WILD-TYPE
  R0            4             73
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESPN MUTATED       0                         0     5
  ESPN WILD-TYPE     2                         5   120
D20V13, multiclass
                           clus
vv                          ESPN MUTATED ESPN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                cls
clus              0  1
  ESPN MUTATED    0  5
  ESPN WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      0    5
  ESPN WILD-TYPE    3   99
                        clus
vv                       ESPN MUTATED ESPN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             99
[1] 2 2
[1] FALSE

Clustering(21) Variable = ATP2C1 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  ATP2C1 MUTATED    1  7
  ATP2C1 WILD-TYPE 61 65
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              126 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               7               65 
$`ATP2C1 MUTATED`
TCGA-2J-AABK TCGA-F2-6879 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-IB-7644 TCGA-IB-7649 
       15.91        10.98        20.19        17.03        12.95        15.35 
TCGA-IB-7651 TCGA-US-A77E 
       19.82        14.14 

$`ATP2C1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.22        22.72        22.26        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       13.84        19.50         0.13        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 
        1.08         0.23        49.38         4.77        21.90        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        27.75        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           10.98             0.13 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           20.19            75.12 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
          15.630           13.155 
[1] "11.0 - 20.2 (15.6)" "0.1 - 75.1 (13.2)" 
[1] "hr=" "1.7"
D21V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ATP2C1 MUTATED          0        0         0         7         0        1
  ATP2C1 WILD-TYPE        4        6        20        92         4        2
D21V3, multiclass
           clus
vv          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              7               92
  STAGE III              0                4
  STAGE IV               1                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP2C1 MUTATED     0   0     8
  ATP2C1 WILD-TYPE   5  13   110
D21V4, multiclass
       clus
vv      ATP2C1 MUTATED ATP2C1 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              8              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    0  8
  ATP2C1 WILD-TYPE 32 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0    8
  ATP2C1 WILD-TYPE   32   96
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0              0               32
  1              8               96
[1] 2 2
[1] FALSE
D21V6, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    4  1
  ATP2C1 WILD-TYPE 58  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      4    1
  ATP2C1 WILD-TYPE   58    2
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0              4               58
  1              1                2
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    3  5
  ATP2C1 WILD-TYPE 59 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      3    5
  ATP2C1 WILD-TYPE   59   69
        clus
vv       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  FEMALE              3               59
  MALE                5               69
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2C1 MUTATED                                     6
  ATP2C1 WILD-TYPE                                 116
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2C1 MUTATED                                       2
  ATP2C1 WILD-TYPE                                     9
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2C1 MUTATED                                                  0
  ATP2C1 WILD-TYPE                                                2
D21V8, multiclass
                                                  clus
vv                                                 ATP2C1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ATP2C1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, continuous
D21V10, continuous
                  vv
clus               R0 R1 R2 RX
  ATP2C1 MUTATED    3  4  0  1
  ATP2C1 WILD-TYPE 74 44  1  2
D21V11, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  R0              3               74
  R1              4               44
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2C1 MUTATED       0                         1     6
  ATP2C1 WILD-TYPE     2                         4   119
D21V13, multiclass
                           clus
vv                          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  6              119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    0  5
  ATP2C1 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0    5
  ATP2C1 WILD-TYPE    3   99
                        clus
vv                       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(22) Variable = FNDC1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2              0  1
  FNDC1 MUTATED    4  9
  FNDC1 WILD-TYPE 58 63
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             13             121 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
              9              63 
$`FNDC1 MUTATED`
TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-A49G 
       22.49        12.95         7.36        12.03         0.69        21.70 
TCGA-IB-7651 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-S4-A8RP 
       19.82         3.85        15.98        14.17         6.02        23.08 
TCGA-YB-A89D 
       11.51 

$`FNDC1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I5 
        9.11        21.44         4.70         3.39         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       23.61        20.84        24.26        28.73        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        12.39        75.12        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8005 
       19.50         0.13        20.19        17.03        23.21         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I 
        9.83        12.43        14.93        17.92        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       21.30         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        0.26         4.73         7.86        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  FNDC1 MUTATED FNDC1 WILD-TYPE 
           0.69            0.13 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
          23.08           75.12 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
          12.95           13.81 
[1] "0.7 - 23.1 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.5"
D22V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FNDC1 MUTATED          0        0         1        11         1        0
  FNDC1 WILD-TYPE        4        6        19        88         3        3
D22V3, multiclass
           clus
vv          FNDC1 MUTATED FNDC1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB            11              88
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  FNDC1 MUTATED     0   1    12
  FNDC1 WILD-TYPE   5  12   106
D22V4, multiclass
       clus
vv      FNDC1 MUTATED FNDC1 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4            12             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                 cls
clus               0  1
  FNDC1 MUTATED    2 11
  FNDC1 WILD-TYPE 30 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      2   11
  FNDC1 WILD-TYPE   30   93
   clus
vv  FNDC1 MUTATED FNDC1 WILD-TYPE
  0             2              30
  1            11              93
[1] 2 2
[1] FALSE
D22V6, binary
                 cls
clus               0  1
  FNDC1 MUTATED    6  0
  FNDC1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      6    0
  FNDC1 WILD-TYPE   56    3
   clus
vv  FNDC1 MUTATED FNDC1 WILD-TYPE
  0             6              56
  1             0               3
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus               0  1
  FNDC1 MUTATED    7  6
  FNDC1 WILD-TYPE 55 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      7    6
  FNDC1 WILD-TYPE   55   68
        clus
vv       FNDC1 MUTATED FNDC1 WILD-TYPE
  FEMALE             7              55
  MALE               6              68
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FNDC1 MUTATED                                    13
  FNDC1 WILD-TYPE                                 109
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FNDC1 MUTATED                                       0
  FNDC1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FNDC1 MUTATED                                                  0
  FNDC1 WILD-TYPE                                                2
D22V8, multiclass
                                                  clus
vv                                                 FNDC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 FNDC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          109
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, continuous
D22V10, continuous
                 vv
clus              R0 R1 R2 RX
  FNDC1 MUTATED    9  4  0  0
  FNDC1 WILD-TYPE 68 44  1  3
D22V11, multiclass
    clus
vv   FNDC1 MUTATED FNDC1 WILD-TYPE
  R0             9              68
  R1             4              44
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FNDC1 MUTATED       0                         0    13
  FNDC1 WILD-TYPE     2                         5   112
D22V13, multiclass
                           clus
vv                          FNDC1 MUTATED FNDC1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                13             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                 cls
clus               0  1
  FNDC1 MUTATED    0 10
  FNDC1 WILD-TYPE  3 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      0   10
  FNDC1 WILD-TYPE    3   94
                        clus
vv                       FNDC1 MUTATED FNDC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            10              94
[1] 2 2
[1] FALSE

Clustering(23) Variable = TMEM91 MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2               0  1
  TMEM91 MUTATED    2  4
  TMEM91 WILD-TYPE 60 68
  TMEM91 MUTATED TMEM91 WILD-TYPE 
               6              128 
  TMEM91 MUTATED TMEM91 WILD-TYPE 
               4               68 
$`TMEM91 MUTATED`
TCGA-FB-A4P6 TCGA-HZ-8315 TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-7897 
       11.93         9.83        10.13        19.82        21.30        15.98 

$`TMEM91 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         3.95        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.92        21.70        16.14         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 
       43.79        15.81        19.66         3.85         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  TMEM91 MUTATED TMEM91 WILD-TYPE 
            9.83             0.13 
  TMEM91 MUTATED TMEM91 WILD-TYPE 
           21.30            75.12 
  TMEM91 MUTATED TMEM91 WILD-TYPE 
          13.955           13.745 
[1] "9.8 - 21.3 (14.0)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D23V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TMEM91 MUTATED          0        0         1         5         0        0
  TMEM91 WILD-TYPE        4        6        19        94         4        3
D23V3, multiclass
           clus
vv          TMEM91 MUTATED TMEM91 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              5               94
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TMEM91 MUTATED     0   0     6
  TMEM91 WILD-TYPE   5  13   112
D23V4, multiclass
       clus
vv      TMEM91 MUTATED TMEM91 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              6              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                  cls
clus                0  1
  TMEM91 MUTATED    1  5
  TMEM91 WILD-TYPE 31 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM91 MUTATED      1    5
  TMEM91 WILD-TYPE   31   99
   clus
vv  TMEM91 MUTATED TMEM91 WILD-TYPE
  0              1               31
  1              5               99
[1] 2 2
[1] FALSE
D23V6, binary
                  cls
clus                0  1
  TMEM91 MUTATED    3  0
  TMEM91 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM91 MUTATED      3    0
  TMEM91 WILD-TYPE   59    3
   clus
vv  TMEM91 MUTATED TMEM91 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D23V7, binary
                  cls
clus                0  1
  TMEM91 MUTATED    4  2
  TMEM91 WILD-TYPE 58 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM91 MUTATED      4    2
  TMEM91 WILD-TYPE   58   72
        clus
vv       TMEM91 MUTATED TMEM91 WILD-TYPE
  FEMALE              4               58
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM91 MUTATED                                     6
  TMEM91 WILD-TYPE                                 116
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM91 MUTATED                                       0
  TMEM91 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM91 MUTATED                                                  0
  TMEM91 WILD-TYPE                                                2
D23V8, multiclass
                                                  clus
vv                                                 TMEM91 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TMEM91 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, continuous
D23V10, continuous
                  vv
clus               R0 R1 R2 RX
  TMEM91 MUTATED    3  2  0  0
  TMEM91 WILD-TYPE 74 46  1  3
D23V11, multiclass
    clus
vv   TMEM91 MUTATED TMEM91 WILD-TYPE
  R0              3               74
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM91 MUTATED       0                         0     6
  TMEM91 WILD-TYPE     2                         5   119
D23V13, multiclass
                           clus
vv                          TMEM91 MUTATED TMEM91 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                  cls
clus                0  1
  TMEM91 MUTATED    0  6
  TMEM91 WILD-TYPE  3 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM91 MUTATED      0    6
  TMEM91 WILD-TYPE    3   98
                        clus
vv                       TMEM91 MUTATED TMEM91 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6               98
[1] 2 2
[1] FALSE

Clustering(24) Variable = SHROOM4 MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2                0  1
  SHROOM4 MUTATED    4  6
  SHROOM4 WILD-TYPE 58 66
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               10               124 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                6                66 
$`SHROOM4 MUTATED`
TCGA-3A-A9I5 TCGA-FB-AAPU TCGA-HZ-7922 TCGA-HZ-8002 TCGA-HZ-8315 TCGA-HZ-A49I 
       53.00        12.53         0.13        12.03         9.83        10.13 
TCGA-HZ-A4BH TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-7897 
        6.38        19.82        21.30        15.98 

$`SHROOM4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43         7.50        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 
       13.84        19.50        20.19        17.03        23.21         0.69 
TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        3.95        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 
        4.04         3.62        43.79        15.81        19.66         3.85 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             0.13              0.23 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            53.00             75.12 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           12.280            13.825 
[1] "0.1 - 53.0 (12.3)" "0.2 - 75.1 (13.8)"
[1] "hr=" "1.1"
D24V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SHROOM4 MUTATED          1        0         2         8         0        0
  SHROOM4 WILD-TYPE        3        6        18        91         4        3
D24V3, multiclass
           clus
vv          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE IA                1                 3
  STAGE IB                0                 6
  STAGE IIA               2                18
  STAGE IIB               8                91
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SHROOM4 MUTATED     1   0    10
  SHROOM4 WILD-TYPE   4  13   108
D24V4, multiclass
       clus
vv      SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1                  1                 4
  T2                  0                13
  T3+T4              10               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    3  8
  SHROOM4 WILD-TYPE 29 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    8
  SHROOM4 WILD-TYPE   29   96
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               3                29
  1               8                96
[1] 2 2
[1] FALSE
D24V6, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    3  0
  SHROOM4 WILD-TYPE 59  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    0
  SHROOM4 WILD-TYPE   59    3
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               3                59
  1               0                 3
[1] 2 2
[1] FALSE
D24V7, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    7  4
  SHROOM4 WILD-TYPE 55 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      7    4
  SHROOM4 WILD-TYPE   55   70
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               7                55
  MALE                 4                70
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SHROOM4 MUTATED                                    11
  SHROOM4 WILD-TYPE                                 111
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SHROOM4 MUTATED                                       0
  SHROOM4 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SHROOM4 MUTATED                                                  0
  SHROOM4 WILD-TYPE                                                2
D24V8, multiclass
                                                  clus
vv                                                 SHROOM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SHROOM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            111
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, continuous
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
D24V10, continuous
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2                37 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-YY-A8LH 
"SHROOM4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SHROOM4 MUTATED    7  4  0  0
  SHROOM4 WILD-TYPE 70 44  1  3
D24V11, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0               7                70
  R1               4                44
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED       1                         0    10
  SHROOM4 WILD-TYPE     1                         5   115
D24V13, multiclass
                           clus
vv                          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  10               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    1  9
  SHROOM4 WILD-TYPE  2 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    9
  SHROOM4 WILD-TYPE    2   95
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               9                95
[1] 2 2
[1] FALSE

Clustering(25) Variable = PABPC1 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    4  5
  PABPC1 WILD-TYPE 58 67
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              125 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               5               67 
$`PABPC1 MUTATED`
TCGA-2J-AABF TCGA-2L-AAQI TCGA-F2-A8YN TCGA-HZ-8317 TCGA-IB-7887 TCGA-IB-A6UG 
       22.72         3.39        17.00        12.43         3.62         1.35 
TCGA-IB-AAUU TCGA-XD-AAUG TCGA-YH-A8SY 
        8.05        13.81        12.76 

$`PABPC1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.22        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
       21.44         4.70        22.49        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
        7.66        19.27         3.12         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        0.69         3.95         9.83        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 
       15.35        19.82        23.80        41.33         4.04        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A7SX 
       14.17         6.02        11.11         7.40         9.44        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUH 
       22.85        27.75        16.80        14.14         0.39        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        66.28         0.69 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
            1.35             0.13 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           22.72            75.12 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           12.43            14.14 
[1] "1.4 - 22.7 (12.4)" "0.1 - 75.1 (14.1)"
[1] "hr=" "1.7"
D25V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PABPC1 MUTATED          0        0         1         6         1        1
  PABPC1 WILD-TYPE        4        6        19        93         3        2
D25V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              6               93
  STAGE III              1                3
  STAGE IV               1                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PABPC1 MUTATED     0   0     9
  PABPC1 WILD-TYPE   5  13   109
D25V4, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              9              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                  cls
clus                0  1
  PABPC1 MUTATED    1  8
  PABPC1 WILD-TYPE 31 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    8
  PABPC1 WILD-TYPE   31   96
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              1               31
  1              8               96
[1] 2 2
[1] FALSE
D25V6, binary
                  cls
clus                0  1
  PABPC1 MUTATED    5  1
  PABPC1 WILD-TYPE 57  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      5    1
  PABPC1 WILD-TYPE   57    2
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              5               57
  1              1                2
[1] 2 2
[1] FALSE
D25V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    4  5
  PABPC1 WILD-TYPE 58 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      4    5
  PABPC1 WILD-TYPE   58   69
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              4               58
  MALE                5               69
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PABPC1 MUTATED                                     8
  PABPC1 WILD-TYPE                                 114
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PABPC1 MUTATED                                       0
  PABPC1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PABPC1 MUTATED                                                  0
  PABPC1 WILD-TYPE                                                2
D25V8, multiclass
                                                  clus
vv                                                 PABPC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 PABPC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           114
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, continuous
D25V10, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABO       TCGA-3A-A9IB 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-YY-A8LH 
"PABPC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PABPC1 MUTATED    2  6  0  0
  PABPC1 WILD-TYPE 75 42  1  3
D25V11, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  R0              2               75
  R1              6               42
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED       0                         0     9
  PABPC1 WILD-TYPE     2                         5   116
D25V13, multiclass
                           clus
vv                          PABPC1 MUTATED PABPC1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                  cls
clus                0  1
  PABPC1 MUTATED    0  7
  PABPC1 WILD-TYPE  3 97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    7
  PABPC1 WILD-TYPE    3   97
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7               97
[1] 2 2
[1] FALSE

Clustering(26) Variable = OGFOD1 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2               0  1
  OGFOD1 MUTATED    3  1
  OGFOD1 WILD-TYPE 59 71
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               4              130 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               1               71 
$`OGFOD1 MUTATED`
TCGA-H6-8124 TCGA-HZ-8519 TCGA-IB-7888 TCGA-IB-8126 
       12.89        14.93        43.79         2.47 

$`OGFOD1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        1.02        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04         3.62        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
            2.47             0.13 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
           43.79            75.12 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
          13.910           13.745 
[1] "2.5 - 43.8 (13.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.5"
D26V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OGFOD1 MUTATED          1        0         1         1         1        0
  OGFOD1 WILD-TYPE        3        6        19        98         3        3
D26V3, multiclass
           clus
vv          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              1               98
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  OGFOD1 MUTATED     1   0     3
  OGFOD1 WILD-TYPE   4  13   115
D26V4, multiclass
       clus
vv      OGFOD1 MUTATED OGFOD1 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                  cls
clus                 0   1
  OGFOD1 MUTATED     2   2
  OGFOD1 WILD-TYPE  30 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      2    2
  OGFOD1 WILD-TYPE   30  102
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              2               30
  1              2              102
[1] 2 2
[1] FALSE
D26V6, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    3  0
  OGFOD1 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      3    0
  OGFOD1 WILD-TYPE   59    3
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    3  1
  OGFOD1 WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      3    1
  OGFOD1 WILD-TYPE   59   73
        clus
vv       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OGFOD1 MUTATED                                     3
  OGFOD1 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OGFOD1 MUTATED                                       1
  OGFOD1 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OGFOD1 MUTATED                                                  0
  OGFOD1 WILD-TYPE                                                2
D26V8, multiclass
                                                  clus
vv                                                 OGFOD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 OGFOD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-A45N       TCGA-HZ-A77Q 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
D26V10, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OGFOD1 MUTATED    3  1  0  0
  OGFOD1 WILD-TYPE 74 47  1  3
D26V11, multiclass
    clus
vv   OGFOD1 MUTATED OGFOD1 WILD-TYPE
  R0              3               74
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGFOD1 MUTATED       0                         1     3
  OGFOD1 WILD-TYPE     2                         4   122
D26V13, multiclass
                           clus
vv                          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                  cls
clus                 0   1
  OGFOD1 MUTATED     0   4
  OGFOD1 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      0    4
  OGFOD1 WILD-TYPE    3  100
                        clus
vv                       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(27) Variable = DCP1B MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2              0  1
  DCP1B MUTATED    3  3
  DCP1B WILD-TYPE 59 69
  DCP1B MUTATED DCP1B WILD-TYPE 
              6             128 
  DCP1B MUTATED DCP1B WILD-TYPE 
              3              69 
$`DCP1B MUTATED`
TCGA-HZ-8003 TCGA-HZ-A49H TCGA-IB-7651 TCGA-IB-7652 TCGA-LB-A7SX TCGA-US-A77G 
        0.69        16.14        19.82        23.80        12.92         0.39 

$`DCP1B WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        21.70        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.44         8.05        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  DCP1B MUTATED DCP1B WILD-TYPE 
           0.39            0.13 
  DCP1B MUTATED DCP1B WILD-TYPE 
          23.80           75.12 
  DCP1B MUTATED DCP1B WILD-TYPE 
         14.530          13.745 
[1] "0.4 - 23.8 (14.5)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D27V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DCP1B MUTATED          0        0         0         7         0        0
  DCP1B WILD-TYPE        4        6        20        92         4        3
D27V3, multiclass
           clus
vv          DCP1B MUTATED DCP1B WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             7              92
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  DCP1B MUTATED     0   0     7
  DCP1B WILD-TYPE   5  13   111
D27V4, multiclass
       clus
vv      DCP1B MUTATED DCP1B WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             7             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                 cls
clus               0  1
  DCP1B MUTATED    0  7
  DCP1B WILD-TYPE 32 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      0    7
  DCP1B WILD-TYPE   32   97
   clus
vv  DCP1B MUTATED DCP1B WILD-TYPE
  0             0              32
  1             7              97
[1] 2 2
[1] FALSE
D27V6, binary
                 cls
clus               0  1
  DCP1B MUTATED    2  0
  DCP1B WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      2    0
  DCP1B WILD-TYPE   60    3
   clus
vv  DCP1B MUTATED DCP1B WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus               0  1
  DCP1B MUTATED    6  1
  DCP1B WILD-TYPE 56 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      6    1
  DCP1B WILD-TYPE   56   73
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  FEMALE             6              56
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DCP1B MUTATED                                     7
  DCP1B WILD-TYPE                                 115
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DCP1B MUTATED                                       0
  DCP1B WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DCP1B MUTATED                                                  0
  DCP1B WILD-TYPE                                                2
D27V8, multiclass
                                                  clus
vv                                                 DCP1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DCP1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, continuous
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A9Q5 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
D27V10, continuous
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A9Q5      TCGA-OE-A75W 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-YY-A8LH 
"DCP1B WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DCP1B MUTATED    5  2  0  0
  DCP1B WILD-TYPE 72 46  1  3
D27V11, multiclass
    clus
vv   DCP1B MUTATED DCP1B WILD-TYPE
  R0             5              72
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DCP1B MUTATED       1                         1     5
  DCP1B WILD-TYPE     1                         4   120
D27V13, multiclass
                           clus
vv                          DCP1B MUTATED DCP1B WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                 cls
clus               0  1
  DCP1B MUTATED    1  6
  DCP1B WILD-TYPE  2 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      1    6
  DCP1B WILD-TYPE    2   98
                        clus
vv                       DCP1B MUTATED DCP1B WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(28) Variable = RBMX MUTATION ANALYSIS
D28V1, survival
                sevent
clus2             0  1
  RBMX MUTATED    2  3
  RBMX WILD-TYPE 60 69
  RBMX MUTATED RBMX WILD-TYPE 
             5            129 
  RBMX MUTATED RBMX WILD-TYPE 
             3             69 
$`RBMX MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-FB-AAQ1 TCGA-HZ-7919 TCGA-YH-A8SY 
       23.97         9.63         4.04        19.50        12.76 

$`RBMX WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
        2.17         2.63        20.61        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.26        15.91        14.47        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       23.54        15.55         5.03         1.02        12.89        13.84 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        66.28         0.69 

  RBMX MUTATED RBMX WILD-TYPE 
          4.04           0.13 
  RBMX MUTATED RBMX WILD-TYPE 
         23.97          75.12 
  RBMX MUTATED RBMX WILD-TYPE 
         12.76          13.81 
[1] "4.0 - 24.0 (12.8)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.2"
D28V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBMX MUTATED          0        0         1         3         1        0
  RBMX WILD-TYPE        4        6        19        96         3        3
D28V3, multiclass
           clus
vv          RBMX MUTATED RBMX WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            3             96
  STAGE III            1              3
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  RBMX MUTATED     0   1     4
  RBMX WILD-TYPE   5  12   114
D28V4, multiclass
       clus
vv      RBMX MUTATED RBMX WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                cls
clus               0   1
  RBMX MUTATED     1   4
  RBMX WILD-TYPE  31 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      1    4
  RBMX WILD-TYPE   31  100
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            1             31
  1            4            100
[1] 2 2
[1] FALSE
D28V6, binary
                cls
clus              0  1
  RBMX MUTATED    3  0
  RBMX WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      3    0
  RBMX WILD-TYPE   59    3
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D28V7, binary
                cls
clus              0  1
  RBMX MUTATED    2  3
  RBMX WILD-TYPE 60 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      2    3
  RBMX WILD-TYPE   60   71
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            2             60
  MALE              3             71
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBMX MUTATED                                     3
  RBMX WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBMX MUTATED                                       1
  RBMX WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBMX MUTATED                                                  0
  RBMX WILD-TYPE                                                2
D28V8, multiclass
                                                  clus
vv                                                 RBMX MUTATED RBMX WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, continuous
D28V10, continuous
                vv
clus             R0 R1 R2 RX
  RBMX MUTATED    2  2  0  0
  RBMX WILD-TYPE 75 46  1  3
D28V11, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            2             75
  R1            2             46
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED       0                         0     5
  RBMX WILD-TYPE     2                         5   120
D28V13, multiclass
                           clus
vv                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                cls
clus               0   1
  RBMX MUTATED     0   3
  RBMX WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    3
  RBMX WILD-TYPE    3  101
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(29) Variable = ZNF880 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  ZNF880 MUTATED    0  3
  ZNF880 WILD-TYPE 62 69
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               3              131 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               3               69 
$`ZNF880 MUTATED`
TCGA-2L-AAQI TCGA-HZ-8315 TCGA-IB-7897 
        3.39         9.83        15.98 

$`ZNF880 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         3.95        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ZNF880 MUTATED ZNF880 WILD-TYPE 
            3.39             0.13 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
           15.98            75.12 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
            9.83            13.81 
[1] "3.4 - 16.0 (9.8)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.6"
D29V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF880 MUTATED          0        0         1         2         0        0
  ZNF880 WILD-TYPE        4        6        19        97         4        3
D29V3, multiclass
           clus
vv          ZNF880 MUTATED ZNF880 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF880 MUTATED     0   0     3
  ZNF880 WILD-TYPE   5  13   115
D29V4, multiclass
       clus
vv      ZNF880 MUTATED ZNF880 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                  cls
clus                 0   1
  ZNF880 MUTATED     1   2
  ZNF880 WILD-TYPE  31 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      1    2
  ZNF880 WILD-TYPE   31  102
   clus
vv  ZNF880 MUTATED ZNF880 WILD-TYPE
  0              1               31
  1              2              102
[1] 2 2
[1] FALSE
D29V6, binary
                  cls
clus                0  1
  ZNF880 MUTATED    1  0
  ZNF880 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      1    0
  ZNF880 WILD-TYPE   61    3
   clus
vv  ZNF880 MUTATED ZNF880 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                0  1
  ZNF880 MUTATED    2  1
  ZNF880 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      2    1
  ZNF880 WILD-TYPE   60   73
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF880 MUTATED                                     3
  ZNF880 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF880 MUTATED                                       0
  ZNF880 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF880 MUTATED                                                  0
  ZNF880 WILD-TYPE                                                2
D29V8, multiclass
                                                  clus
vv                                                 ZNF880 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF880 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, continuous
D29V10, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF880 MUTATED    1  2  0  0
  ZNF880 WILD-TYPE 76 46  1  3
D29V11, multiclass
    clus
vv   ZNF880 MUTATED ZNF880 WILD-TYPE
  R0              1               76
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF880 MUTATED       0                         0     3
  ZNF880 WILD-TYPE     2                         5   122
D29V13, multiclass
                           clus
vv                          ZNF880 MUTATED ZNF880 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                  cls
clus                 0   1
  ZNF880 MUTATED     0   2
  ZNF880 WILD-TYPE   3 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      0    2
  ZNF880 WILD-TYPE    3  102
                        clus
vv                       ZNF880 MUTATED ZNF880 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(30) Variable = UBAC1 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  UBAC1 MUTATED    2  3
  UBAC1 WILD-TYPE 60 69
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             129 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              3              69 
$`UBAC1 MUTATED`
TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8005 TCGA-IB-7886 TCGA-M8-A5N4 
        0.13        17.03         3.95         4.04        19.20 

$`UBAC1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8001 
        1.02        12.89        13.84        19.50        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 
       21.90        15.35        19.82        23.80        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        9.44         8.05        12.92        12.46        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  UBAC1 MUTATED UBAC1 WILD-TYPE 
           0.13            0.23 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
          19.20           75.12 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
           4.04           13.81 
[1] "0.1 - 19.2 (4.0)"  "0.2 - 75.1 (13.8)"
[1] "hr=" "2.2"
D30V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UBAC1 MUTATED          0        0         1         4         0        0
  UBAC1 WILD-TYPE        4        6        19        95         4        3
D30V3, multiclass
           clus
vv          UBAC1 MUTATED UBAC1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  UBAC1 MUTATED     0   0     5
  UBAC1 WILD-TYPE   5  13   113
D30V4, multiclass
       clus
vv      UBAC1 MUTATED UBAC1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                 cls
clus                0   1
  UBAC1 MUTATED     1   4
  UBAC1 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      1    4
  UBAC1 WILD-TYPE   31  100
   clus
vv  UBAC1 MUTATED UBAC1 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D30V6, binary
                 cls
clus               0  1
  UBAC1 MUTATED    2  0
  UBAC1 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      2    0
  UBAC1 WILD-TYPE   60    3
   clus
vv  UBAC1 MUTATED UBAC1 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus               0  1
  UBAC1 MUTATED    2  3
  UBAC1 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      2    3
  UBAC1 WILD-TYPE   60   71
        clus
vv       UBAC1 MUTATED UBAC1 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBAC1 MUTATED                                     5
  UBAC1 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBAC1 MUTATED                                       0
  UBAC1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBAC1 MUTATED                                                  0
  UBAC1 WILD-TYPE                                                2
D30V8, multiclass
                                                  clus
vv                                                 UBAC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 UBAC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, continuous
[1] "Remove cluster labels:" "UBAC1 MUTATED"         
clus
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7887 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "UBAC1 MUTATED"         
clus
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  UBAC1 MUTATED    1  3  0  1
  UBAC1 WILD-TYPE 76 45  1  2
D30V11, multiclass
    clus
vv   UBAC1 MUTATED UBAC1 WILD-TYPE
  R0             1              76
  R1             3              45
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBAC1 MUTATED       0                         1     3
  UBAC1 WILD-TYPE     2                         4   122
D30V13, multiclass
                           clus
vv                          UBAC1 MUTATED UBAC1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                 cls
clus                0   1
  UBAC1 MUTATED     0   4
  UBAC1 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      0    4
  UBAC1 WILD-TYPE    3  100
                        clus
vv                       UBAC1 MUTATED UBAC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(31) Variable = CASQ2 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2              0  1
  CASQ2 MUTATED    5  2
  CASQ2 WILD-TYPE 57 70
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              7             127 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              2              70 
$`CASQ2 MUTATED`
TCGA-H6-8124 TCGA-HZ-A4BH TCGA-HZ-A77Q TCGA-IB-7647 TCGA-IB-7887 TCGA-LB-A8F3 
       12.89         6.38         1.08        21.90         3.62        12.46 
TCGA-US-A776 
       27.75 

$`CASQ2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        1.02        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK 
       14.93        17.92        21.70        16.14        10.13        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 
       15.35        19.82        23.80        41.33         4.04        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        8.05        12.92        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       23.08        22.85        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  CASQ2 MUTATED CASQ2 WILD-TYPE 
           1.08            0.13 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
          27.75           75.12 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
          12.46           13.84 
[1] "1.1 - 27.8 (12.5)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.6"
D31V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CASQ2 MUTATED          0        0         2         5         0        0
  CASQ2 WILD-TYPE        4        6        18        94         4        3
D31V3, multiclass
           clus
vv          CASQ2 MUTATED CASQ2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CASQ2 MUTATED     0   0     7
  CASQ2 WILD-TYPE   5  13   111
D31V4, multiclass
       clus
vv      CASQ2 MUTATED CASQ2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             7             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                 cls
clus               0  1
  CASQ2 MUTATED    2  5
  CASQ2 WILD-TYPE 30 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      2    5
  CASQ2 WILD-TYPE   30   99
   clus
vv  CASQ2 MUTATED CASQ2 WILD-TYPE
  0             2              30
  1             5              99
[1] 2 2
[1] FALSE
D31V6, binary
                 cls
clus               0  1
  CASQ2 MUTATED    3  0
  CASQ2 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      3    0
  CASQ2 WILD-TYPE   59    3
   clus
vv  CASQ2 MUTATED CASQ2 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus               0  1
  CASQ2 MUTATED    4  3
  CASQ2 WILD-TYPE 58 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      4    3
  CASQ2 WILD-TYPE   58   71
        clus
vv       CASQ2 MUTATED CASQ2 WILD-TYPE
  FEMALE             4              58
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CASQ2 MUTATED                                     5
  CASQ2 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CASQ2 MUTATED                                       1
  CASQ2 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CASQ2 MUTATED                                                  1
  CASQ2 WILD-TYPE                                                1
D31V8, multiclass
                                                  clus
vv                                                 CASQ2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 CASQ2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, continuous
D31V10, continuous
[1] "Remove cluster labels:" "CASQ2 MUTATED"         
clus
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
     TCGA-YY-A8LH 
"CASQ2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CASQ2 MUTATED    4  3  0  0
  CASQ2 WILD-TYPE 73 45  1  3
D31V11, multiclass
    clus
vv   CASQ2 MUTATED CASQ2 WILD-TYPE
  R0             4              73
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASQ2 MUTATED       0                         1     6
  CASQ2 WILD-TYPE     2                         4   119
D31V13, multiclass
                           clus
vv                          CASQ2 MUTATED CASQ2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                 cls
clus               0  1
  CASQ2 MUTATED    0  6
  CASQ2 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      0    6
  CASQ2 WILD-TYPE    3   98
                        clus
vv                       CASQ2 MUTATED CASQ2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(32) Variable = ZNF678 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2               0  1
  ZNF678 MUTATED    0  5
  ZNF678 WILD-TYPE 62 67
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              129 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5               67 
$`ZNF678 MUTATED`
TCGA-HZ-7925 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-IB-7649 TCGA-IB-7651 
       20.19        12.03         3.95        15.35        19.82 

$`ZNF678 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       23.21         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  ZNF678 MUTATED ZNF678 WILD-TYPE 
            3.95             0.13 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
           20.19            75.12 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
           15.35            13.68 
[1] "4.0 - 20.2 (15.3)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.2"
D32V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF678 MUTATED          0        0         0         5         0        0
  ZNF678 WILD-TYPE        4        6        20        94         4        3
D32V3, multiclass
           clus
vv          ZNF678 MUTATED ZNF678 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              5               94
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF678 MUTATED     0   0     5
  ZNF678 WILD-TYPE   5  13   113
D32V4, multiclass
       clus
vv      ZNF678 MUTATED ZNF678 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                  cls
clus                0  1
  ZNF678 MUTATED    0  5
  ZNF678 WILD-TYPE 32 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      0    5
  ZNF678 WILD-TYPE   32   99
   clus
vv  ZNF678 MUTATED ZNF678 WILD-TYPE
  0              0               32
  1              5               99
[1] 2 2
[1] FALSE
D32V6, binary
                  cls
clus                0  1
  ZNF678 MUTATED    2  0
  ZNF678 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      2    0
  ZNF678 WILD-TYPE   60    3
   clus
vv  ZNF678 MUTATED ZNF678 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                0  1
  ZNF678 MUTATED    2  3
  ZNF678 WILD-TYPE 60 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      2    3
  ZNF678 WILD-TYPE   60   71
        clus
vv       ZNF678 MUTATED ZNF678 WILD-TYPE
  FEMALE              2               60
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF678 MUTATED                                     5
  ZNF678 WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF678 MUTATED                                       0
  ZNF678 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF678 MUTATED                                                  0
  ZNF678 WILD-TYPE                                                2
D32V8, multiclass
                                                  clus
vv                                                 ZNF678 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF678 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, continuous
[1] "Remove cluster labels:" "ZNF678 MUTATED"        
clus
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
D32V10, continuous
[1] "Remove cluster labels:" "ZNF678 MUTATED"        
clus
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-YY-A8LH 
"ZNF678 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF678 MUTATED    3  2  0  0
  ZNF678 WILD-TYPE 74 46  1  3
D32V11, multiclass
    clus
vv   ZNF678 MUTATED ZNF678 WILD-TYPE
  R0              3               74
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF678 MUTATED       0                         0     4
  ZNF678 WILD-TYPE     2                         5   121
D32V13, multiclass
                           clus
vv                          ZNF678 MUTATED ZNF678 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                  cls
clus                 0   1
  ZNF678 MUTATED     0   4
  ZNF678 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      0    4
  ZNF678 WILD-TYPE    3  100
                        clus
vv                       ZNF678 MUTATED ZNF678 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(33) Variable = RBM12 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  RBM12 MUTATED    2  3
  RBM12 WILD-TYPE 60 69
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             129 
  RBM12 MUTATED RBM12 WILD-TYPE 
              3              69 
$`RBM12 MUTATED`
TCGA-3A-A9IZ TCGA-F2-A8YN TCGA-FB-AAQ3 TCGA-IB-AAUP TCGA-RB-A7B8 
       10.13        17.00         1.02        14.17        15.32 

$`RBM12 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        34.09        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98         7.66        19.27         3.12         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-S4-A8RM 
        8.78        15.45        13.68         3.12         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  RBM12 MUTATED RBM12 WILD-TYPE 
           1.02            0.13 
  RBM12 MUTATED RBM12 WILD-TYPE 
          17.00           75.12 
  RBM12 MUTATED RBM12 WILD-TYPE 
          14.17           13.68 
[1] "1.0 - 17.0 (14.2)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.7"
D33V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM12 MUTATED          0        0         1         4         0        0
  RBM12 WILD-TYPE        4        6        19        95         4        3
D33V3, multiclass
           clus
vv          RBM12 MUTATED RBM12 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RBM12 MUTATED     0   0     5
  RBM12 WILD-TYPE   5  13   113
D33V4, multiclass
       clus
vv      RBM12 MUTATED RBM12 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                 cls
clus                0   1
  RBM12 MUTATED     1   4
  RBM12 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      1    4
  RBM12 WILD-TYPE   31  100
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D33V6, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  0
  RBM12 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    0
  RBM12 WILD-TYPE   60    3
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  3
  RBM12 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    3
  RBM12 WILD-TYPE   60   71
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM12 MUTATED                                     4
  RBM12 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM12 MUTATED                                       1
  RBM12 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM12 MUTATED                                                  0
  RBM12 WILD-TYPE                                                2
D33V8, multiclass
                                                  clus
vv                                                 RBM12 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RBM12 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, continuous
[1] "Remove cluster labels:" "RBM12 MUTATED"         
clus
  RBM12 MUTATED RBM12 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
D33V10, continuous
                 vv
clus              R0 R1 R2 RX
  RBM12 MUTATED    2  3  0  0
  RBM12 WILD-TYPE 75 45  1  3
D33V11, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0             2              75
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM12 MUTATED       0                         0     5
  RBM12 WILD-TYPE     2                         5   120
D33V13, multiclass
                           clus
vv                          RBM12 MUTATED RBM12 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                 cls
clus                0   1
  RBM12 MUTATED     1   4
  RBM12 WILD-TYPE   2 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      1    4
  RBM12 WILD-TYPE    2  100
                        clus
vv                       RBM12 MUTATED RBM12 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(34) Variable = VWA3A MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2              0  1
  VWA3A MUTATED    1  4
  VWA3A WILD-TYPE 61 68
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             129 
  VWA3A MUTATED VWA3A WILD-TYPE 
              4              68 
$`VWA3A MUTATED`
TCGA-2J-AAB8 TCGA-HZ-8002 TCGA-HZ-8636 TCGA-IB-7644 TCGA-IB-7651 
        2.63        12.03        17.92        12.95        19.82 

$`VWA3A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         1.08         0.23        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  VWA3A MUTATED VWA3A WILD-TYPE 
           2.63            0.13 
  VWA3A MUTATED VWA3A WILD-TYPE 
          19.82           75.12 
  VWA3A MUTATED VWA3A WILD-TYPE 
          12.95           13.81 
[1] "2.6 - 19.8 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.9"
D34V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  VWA3A MUTATED          0        0         0         3         0        2
  VWA3A WILD-TYPE        4        6        20        96         4        1
D34V3, multiclass
           clus
vv          VWA3A MUTATED VWA3A WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              2               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  VWA3A MUTATED     0   0     5
  VWA3A WILD-TYPE   5  13   113
D34V4, multiclass
       clus
vv      VWA3A MUTATED VWA3A WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                 cls
clus                0   1
  VWA3A MUTATED     1   4
  VWA3A WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      1    4
  VWA3A WILD-TYPE   31  100
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D34V6, binary
                 cls
clus               0  1
  VWA3A MUTATED    2  2
  VWA3A WILD-TYPE 60  1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      2    2
  VWA3A WILD-TYPE   60    1
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0             2              60
  1             2               1
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus               0  1
  VWA3A MUTATED    3  2
  VWA3A WILD-TYPE 59 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      3    2
  VWA3A WILD-TYPE   59   72
        clus
vv       VWA3A MUTATED VWA3A WILD-TYPE
  FEMALE             3              59
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VWA3A MUTATED                                     5
  VWA3A WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VWA3A MUTATED                                       0
  VWA3A WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VWA3A MUTATED                                                  0
  VWA3A WILD-TYPE                                                2
D34V8, multiclass
                                                  clus
vv                                                 VWA3A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 VWA3A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, continuous
[1] "Remove cluster labels:" "VWA3A MUTATED"         
clus
  VWA3A MUTATED VWA3A WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7649 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
D34V10, continuous
[1] "Remove cluster labels:" "VWA3A MUTATED"         
clus
  VWA3A MUTATED VWA3A WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-YY-A8LH 
"VWA3A WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  VWA3A MUTATED    2  3  0  0
  VWA3A WILD-TYPE 75 45  1  3
D34V11, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  R0             2              75
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VWA3A MUTATED       0                         0     5
  VWA3A WILD-TYPE     2                         5   120
D34V13, multiclass
                           clus
vv                          VWA3A MUTATED VWA3A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                 cls
clus                0   1
  VWA3A MUTATED     0   4
  VWA3A WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      0    4
  VWA3A WILD-TYPE    3  100
                        clus
vv                       VWA3A MUTATED VWA3A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(35) Variable = NBPF16 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2               0  1
  NBPF16 MUTATED    2  4
  NBPF16 WILD-TYPE 60 68
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               6              128 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               4               68 
$`NBPF16 MUTATED`
TCGA-2J-AABV TCGA-2L-AAQE TCGA-FB-AAPU TCGA-IB-7897 TCGA-IB-AAUP TCGA-RB-AA9M 
       21.44        22.49        12.53        15.98        14.17         9.40 

$`NBPF16 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        9.11         4.70         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ 
       24.07        14.76        12.43         7.50        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  NBPF16 MUTATED NBPF16 WILD-TYPE 
            9.40             0.13 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
           22.49            75.12 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
          15.075           13.500 
[1] "9.4 - 22.5 (15.1)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.2"
D35V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NBPF16 MUTATED          0        0         1         5         0        0
  NBPF16 WILD-TYPE        4        6        19        94         4        3
D35V3, multiclass
           clus
vv          NBPF16 MUTATED NBPF16 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              5               94
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  NBPF16 MUTATED     1   0     5
  NBPF16 WILD-TYPE   4  13   113
D35V4, multiclass
       clus
vv      NBPF16 MUTATED NBPF16 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                  cls
clus                0  1
  NBPF16 MUTATED    1  5
  NBPF16 WILD-TYPE 31 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      1    5
  NBPF16 WILD-TYPE   31   99
   clus
vv  NBPF16 MUTATED NBPF16 WILD-TYPE
  0              1               31
  1              5               99
[1] 2 2
[1] FALSE
D35V6, binary
                  cls
clus                0  1
  NBPF16 MUTATED    4  0
  NBPF16 WILD-TYPE 58  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      4    0
  NBPF16 WILD-TYPE   58    3
   clus
vv  NBPF16 MUTATED NBPF16 WILD-TYPE
  0              4               58
  1              0                3
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                0  1
  NBPF16 MUTATED    2  4
  NBPF16 WILD-TYPE 60 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      2    4
  NBPF16 WILD-TYPE   60   70
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  FEMALE              2               60
  MALE                4               70
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF16 MUTATED                                     6
  NBPF16 WILD-TYPE                                 116
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF16 MUTATED                                       0
  NBPF16 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF16 MUTATED                                                  0
  NBPF16 WILD-TYPE                                                2
D35V8, multiclass
                                                  clus
vv                                                 NBPF16 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 NBPF16 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, continuous
[1] "Remove cluster labels:" "NBPF16 MUTATED"        
clus
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2L-AAQA       TCGA-3A-A9I9       TCGA-3A-A9IB 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A4P5       TCGA-FB-A4P6 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q       TCGA-HZ-A8P0 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
D35V10, continuous
                  vv
clus               R0 R1 R2 RX
  NBPF16 MUTATED    3  3  0  0
  NBPF16 WILD-TYPE 74 45  1  3
D35V11, multiclass
    clus
vv   NBPF16 MUTATED NBPF16 WILD-TYPE
  R0              3               74
  R1              3               45
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF16 MUTATED       1                         0     5
  NBPF16 WILD-TYPE     1                         5   120
D35V13, multiclass
                           clus
vv                          NBPF16 MUTATED NBPF16 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                  cls
clus                 0   1
  NBPF16 MUTATED     0   4
  NBPF16 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      0    4
  NBPF16 WILD-TYPE    3  100
                        clus
vv                       NBPF16 MUTATED NBPF16 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(36) Variable = PARP10 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  PARP10 MUTATED    3  2
  PARP10 WILD-TYPE 59 70
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              129 
  PARP10 MUTATED PARP10 WILD-TYPE 
               2               70 
$`PARP10 MUTATED`
TCGA-3A-A9IH TCGA-HZ-7922 TCGA-IB-7651 TCGA-IB-7887 TCGA-Z5-AAPL 
       28.73         0.13        19.82         3.62         0.69 

$`PARP10 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  PARP10 MUTATED PARP10 WILD-TYPE 
            0.13             0.23 
  PARP10 MUTATED PARP10 WILD-TYPE 
           28.73            75.12 
  PARP10 MUTATED PARP10 WILD-TYPE 
            3.62            13.81 
[1] "0.1 - 28.7 (3.6)"  "0.2 - 75.1 (13.8)"
[1] "hr=" "1"  
D36V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PARP10 MUTATED          1        0         1         3         0        0
  PARP10 WILD-TYPE        3        6        19        96         4        3
D36V3, multiclass
           clus
vv          PARP10 MUTATED PARP10 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PARP10 MUTATED     1   0     4
  PARP10 WILD-TYPE   4  13   114
D36V4, multiclass
       clus
vv      PARP10 MUTATED PARP10 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                  cls
clus                 0   1
  PARP10 MUTATED     2   3
  PARP10 WILD-TYPE  30 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      2    3
  PARP10 WILD-TYPE   30  101
   clus
vv  PARP10 MUTATED PARP10 WILD-TYPE
  0              2               30
  1              3              101
[1] 2 2
[1] FALSE
D36V6, binary
                  cls
clus                0  1
  PARP10 MUTATED    3  0
  PARP10 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      3    0
  PARP10 WILD-TYPE   59    3
   clus
vv  PARP10 MUTATED PARP10 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                0  1
  PARP10 MUTATED    5  0
  PARP10 WILD-TYPE 57 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      5    0
  PARP10 WILD-TYPE   57   74
        clus
vv       PARP10 MUTATED PARP10 WILD-TYPE
  FEMALE              5               57
  MALE                0               74
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PARP10 MUTATED                                     5
  PARP10 WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PARP10 MUTATED                                       0
  PARP10 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PARP10 MUTATED                                                  0
  PARP10 WILD-TYPE                                                2
D36V8, multiclass
                                                  clus
vv                                                 PARP10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 PARP10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, continuous
[1] "Remove cluster labels:" "PARP10 MUTATED"        
clus
  PARP10 MUTATED PARP10 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
D36V10, continuous
[1] "Remove cluster labels:" "PARP10 MUTATED"        
clus
  PARP10 MUTATED PARP10 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PARP10 MUTATED    4  1  0  0
  PARP10 WILD-TYPE 73 47  1  3
D36V11, multiclass
    clus
vv   PARP10 MUTATED PARP10 WILD-TYPE
  R0              4               73
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARP10 MUTATED       0                         0     5
  PARP10 WILD-TYPE     2                         5   120
D36V13, multiclass
                           clus
vv                          PARP10 MUTATED PARP10 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                  cls
clus                0  1
  PARP10 MUTATED    0  5
  PARP10 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      0    5
  PARP10 WILD-TYPE    3   99
                        clus
vv                       PARP10 MUTATED PARP10 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(37) Variable = TGFBR2 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2               0  1
  TGFBR2 MUTATED    2  6
  TGFBR2 WILD-TYPE 60 66
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              126 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               6               66 
$`TGFBR2 MUTATED`
TCGA-2J-AAB1 TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9IC TCGA-IB-7651 TCGA-IB-7885 
        2.17        12.95         9.60        24.26        19.82        41.33 
TCGA-IB-A5SO TCGA-Z5-AAPL 
       12.00         0.69 

$`TGFBR2 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-3A-A9I5 TCGA-3A-A9I7 
       21.44         4.70        22.49         3.39        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       20.84         7.36        28.73        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       12.39        75.12        71.74        10.98         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM 
        3.12        17.00         5.88        11.93        24.07        14.76 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.43         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 
        4.04         5.03         1.02        12.89        13.84        19.50 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.35        23.80         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            0.69             0.13 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           41.33            75.12 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          12.475           13.825 
[1] "0.7 - 41.3 (12.5)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.4"
D37V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TGFBR2 MUTATED          0        0         1         6         1        0
  TGFBR2 WILD-TYPE        4        6        19        93         3        3
D37V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              6               93
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TGFBR2 MUTATED     0   0     8
  TGFBR2 WILD-TYPE   5  13   110
D37V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              8              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    2  6
  TGFBR2 WILD-TYPE 30 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      2    6
  TGFBR2 WILD-TYPE   30   98
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              2               30
  1              6               98
[1] 2 2
[1] FALSE
D37V6, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    5  0
  TGFBR2 WILD-TYPE 57  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      5    0
  TGFBR2 WILD-TYPE   57    3
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              5               57
  1              0                3
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    5  3
  TGFBR2 WILD-TYPE 57 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      5    3
  TGFBR2 WILD-TYPE   57   71
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              5               57
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR2 MUTATED                                     7
  TGFBR2 WILD-TYPE                                 115
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR2 MUTATED                                       1
  TGFBR2 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR2 MUTATED                                                  0
  TGFBR2 WILD-TYPE                                                2
D37V8, multiclass
                                                  clus
vv                                                 TGFBR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TGFBR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, continuous
D37V10, continuous
                  vv
clus               R0 R1 R2 RX
  TGFBR2 MUTATED    6  1  0  1
  TGFBR2 WILD-TYPE 71 47  1  2
D37V11, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0              6               71
  R1              1               47
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED       0                         0     8
  TGFBR2 WILD-TYPE     2                         5   117
D37V13, multiclass
                           clus
vv                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0   4
  TGFBR2 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    4
  TGFBR2 WILD-TYPE    3  100
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(38) Variable = HACL1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2              0  1
  HACL1 MUTATED    1  3
  HACL1 WILD-TYPE 61 69
  HACL1 MUTATED HACL1 WILD-TYPE 
              4             130 
  HACL1 MUTATED HACL1 WILD-TYPE 
              3              69 
$`HACL1 MUTATED`
TCGA-HZ-7919 TCGA-HZ-8003 TCGA-IB-7645 TCGA-S4-A8RP 
       19.50         0.69        49.38        23.08 

$`HACL1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        1.02        12.89        13.84         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        12.95         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        9.40        21.24        17.26        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  HACL1 MUTATED HACL1 WILD-TYPE 
           0.69            0.13 
  HACL1 MUTATED HACL1 WILD-TYPE 
          49.38           75.12 
  HACL1 MUTATED HACL1 WILD-TYPE 
          21.29           13.50 
[1] "0.7 - 49.4 (21.3)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.2"
D38V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HACL1 MUTATED          0        0         0         4         0        0
  HACL1 WILD-TYPE        4        6        20        95         4        3
D38V3, multiclass
           clus
vv          HACL1 MUTATED HACL1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  HACL1 MUTATED     0   0     4
  HACL1 WILD-TYPE   5  13   114
D38V4, multiclass
       clus
vv      HACL1 MUTATED HACL1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                 cls
clus                0   1
  HACL1 MUTATED     0   4
  HACL1 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      0    4
  HACL1 WILD-TYPE   32  100
   clus
vv  HACL1 MUTATED HACL1 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D38V6, binary
                 cls
clus               0  1
  HACL1 MUTATED    2  0
  HACL1 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      2    0
  HACL1 WILD-TYPE   60    3
   clus
vv  HACL1 MUTATED HACL1 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus               0  1
  HACL1 MUTATED    4  0
  HACL1 WILD-TYPE 58 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      4    0
  HACL1 WILD-TYPE   58   74
        clus
vv       HACL1 MUTATED HACL1 WILD-TYPE
  FEMALE             4              58
  MALE               0              74
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HACL1 MUTATED                                     4
  HACL1 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HACL1 MUTATED                                       0
  HACL1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HACL1 MUTATED                                                  0
  HACL1 WILD-TYPE                                                2
D38V8, multiclass
                                                  clus
vv                                                 HACL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 HACL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, continuous
[1] "Remove cluster labels:" "HACL1 MUTATED"         
clus
  HACL1 MUTATED HACL1 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
D38V10, continuous
                 vv
clus              R0 R1 R2 RX
  HACL1 MUTATED    3  1  0  0
  HACL1 WILD-TYPE 74 47  1  3
D38V11, multiclass
    clus
vv   HACL1 MUTATED HACL1 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HACL1 MUTATED       0                         0     3
  HACL1 WILD-TYPE     2                         5   122
D38V13, multiclass
                           clus
vv                          HACL1 MUTATED HACL1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                 cls
clus                0   1
  HACL1 MUTATED     0   2
  HACL1 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      0    2
  HACL1 WILD-TYPE    3  102
                        clus
vv                       HACL1 MUTATED HACL1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(39) Variable = PRKRA MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2              0  1
  PRKRA MUTATED    1  2
  PRKRA WILD-TYPE 61 70
  PRKRA MUTATED PRKRA WILD-TYPE 
              3             131 
  PRKRA MUTATED PRKRA WILD-TYPE 
              2              70 
$`PRKRA MUTATED`
TCGA-FB-AAQ1 TCGA-IB-7891 TCGA-RB-A7B8 
        4.04        21.30        15.32 

$`PRKRA WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        23.54        15.55         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  PRKRA MUTATED PRKRA WILD-TYPE 
           4.04            0.13 
  PRKRA MUTATED PRKRA WILD-TYPE 
          21.30           75.12 
  PRKRA MUTATED PRKRA WILD-TYPE 
          15.32           13.68 
[1] "4.0 - 21.3 (15.3)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D39V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PRKRA MUTATED          0        0         0         3         0        0
  PRKRA WILD-TYPE        4        6        20        96         4        3
D39V3, multiclass
           clus
vv          PRKRA MUTATED PRKRA WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PRKRA MUTATED     0   0     3
  PRKRA WILD-TYPE   5  13   115
D39V4, multiclass
       clus
vv      PRKRA MUTATED PRKRA WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                 cls
clus                0   1
  PRKRA MUTATED     0   3
  PRKRA WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      0    3
  PRKRA WILD-TYPE   32  101
   clus
vv  PRKRA MUTATED PRKRA WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D39V6, binary
                 cls
clus               0  1
  PRKRA MUTATED    1  0
  PRKRA WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      1    0
  PRKRA WILD-TYPE   61    3
   clus
vv  PRKRA MUTATED PRKRA WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus               0  1
  PRKRA MUTATED    2  1
  PRKRA WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      2    1
  PRKRA WILD-TYPE   60   73
        clus
vv       PRKRA MUTATED PRKRA WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRKRA MUTATED                                     2
  PRKRA WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRKRA MUTATED                                       1
  PRKRA WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRKRA MUTATED                                                  0
  PRKRA WILD-TYPE                                                2
D39V8, multiclass
                                                  clus
vv                                                 PRKRA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PRKRA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, continuous
[1] "Remove cluster labels:" "PRKRA MUTATED"         
clus
  PRKRA MUTATED PRKRA WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
D39V10, continuous
[1] "Remove cluster labels:" "PRKRA MUTATED"         
clus
  PRKRA MUTATED PRKRA WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRKRA MUTATED    2  1  0  0
  PRKRA WILD-TYPE 75 47  1  3
D39V11, multiclass
    clus
vv   PRKRA MUTATED PRKRA WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKRA MUTATED       0                         0     3
  PRKRA WILD-TYPE     2                         5   122
D39V13, multiclass
                           clus
vv                          PRKRA MUTATED PRKRA WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                 cls
clus                0   1
  PRKRA MUTATED     0   3
  PRKRA WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      0    3
  PRKRA WILD-TYPE    3  101
                        clus
vv                       PRKRA MUTATED PRKRA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(40) Variable = SORBS2 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2               0  1
  SORBS2 MUTATED    1  3
  SORBS2 WILD-TYPE 61 69
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               4              130 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               3               69 
$`SORBS2 MUTATED`
TCGA-F2-A8YN TCGA-FB-AAPU TCGA-IB-7651 TCGA-RB-A7B8 
       17.00        12.53        19.82        15.32 

$`SORBS2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 
       71.74        10.98         7.66        19.27         3.12         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43         7.50        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       19.20         8.78        15.45        13.68         3.12         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
           12.53             0.13 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           19.82            75.12 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           16.16            13.50 
[1] "12.5 - 19.8 (16.2)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.4"
D40V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SORBS2 MUTATED          0        0         2         3         0        0
  SORBS2 WILD-TYPE        4        6        18        96         4        3
D40V3, multiclass
           clus
vv          SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              2               18
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  SORBS2 MUTATED     0   0     5
  SORBS2 WILD-TYPE   5  13   113
D40V4, multiclass
       clus
vv      SORBS2 MUTATED SORBS2 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                  cls
clus                 0   1
  SORBS2 MUTATED     2   3
  SORBS2 WILD-TYPE  30 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2    3
  SORBS2 WILD-TYPE   30  101
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              2               30
  1              3              101
[1] 2 2
[1] FALSE
D40V6, binary
                  cls
clus                0  1
  SORBS2 MUTATED    2  0
  SORBS2 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2    0
  SORBS2 WILD-TYPE   60    3
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                0  1
  SORBS2 MUTATED    3  2
  SORBS2 WILD-TYPE 59 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      3    2
  SORBS2 WILD-TYPE   59   72
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE              3               59
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORBS2 MUTATED                                     4
  SORBS2 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORBS2 MUTATED                                       1
  SORBS2 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORBS2 MUTATED                                                  0
  SORBS2 WILD-TYPE                                                2
D40V8, multiclass
                                                  clus
vv                                                 SORBS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 SORBS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, continuous
D40V10, continuous
[1] "Remove cluster labels:" "SORBS2 MUTATED"        
clus
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P1       TCGA-IB-7644 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
      TCGA-YY-A8LH 
"SORBS2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SORBS2 MUTATED    3  2  0  0
  SORBS2 WILD-TYPE 74 46  1  3
D40V11, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  R0              3               74
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORBS2 MUTATED       1                         0     4
  SORBS2 WILD-TYPE     1                         5   121
D40V13, multiclass
                           clus
vv                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                  cls
clus                0  1
  SORBS2 MUTATED    0  5
  SORBS2 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      0    5
  SORBS2 WILD-TYPE    3   99
                        clus
vv                       SORBS2 MUTATED SORBS2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(41) Variable = CD86 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2             0  1
  CD86 MUTATED    4  2
  CD86 WILD-TYPE 58 70
  CD86 MUTATED CD86 WILD-TYPE 
             6            128 
  CD86 MUTATED CD86 WILD-TYPE 
             2             70 
$`CD86 MUTATED`
TCGA-3A-A9IC TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-AAUU TCGA-S4-A8RM 
       24.26        17.00        19.82        23.80         8.05        21.24 

$`CD86 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84         7.36        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98         7.66        19.27         3.12         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.44        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32         9.40        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  CD86 MUTATED CD86 WILD-TYPE 
          8.05           0.13 
  CD86 MUTATED CD86 WILD-TYPE 
         24.26          75.12 
  CD86 MUTATED CD86 WILD-TYPE 
        20.530         13.155 
[1] "8.1 - 24.3 (20.5)" "0.1 - 75.1 (13.2)"
[1] "hr=" "2.5"
D41V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CD86 MUTATED          0        0         1         5         0        0
  CD86 WILD-TYPE        4        6        19        94         4        3
D41V3, multiclass
           clus
vv          CD86 MUTATED CD86 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  CD86 MUTATED     0   0     6
  CD86 WILD-TYPE   5  13   112
D41V4, multiclass
       clus
vv      CD86 MUTATED CD86 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            6            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                cls
clus              0  1
  CD86 MUTATED    1  5
  CD86 WILD-TYPE 31 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      1    5
  CD86 WILD-TYPE   31   99
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            1             31
  1            5             99
[1] 2 2
[1] FALSE
D41V6, binary
                cls
clus              0  1
  CD86 MUTATED    4  0
  CD86 WILD-TYPE 58  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      4    0
  CD86 WILD-TYPE   58    3
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            4             58
  1            0              3
[1] 2 2
[1] FALSE
D41V7, binary
                cls
clus              0  1
  CD86 MUTATED    3  3
  CD86 WILD-TYPE 59 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      3    3
  CD86 WILD-TYPE   59   71
        clus
vv       CD86 MUTATED CD86 WILD-TYPE
  FEMALE            3             59
  MALE              3             71
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD86 MUTATED                                     6
  CD86 WILD-TYPE                                 116
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD86 MUTATED                                       0
  CD86 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD86 MUTATED                                                  0
  CD86 WILD-TYPE                                                2
D41V8, multiclass
                                                  clus
vv                                                 CD86 MUTATED CD86 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6            116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, continuous
D41V10, continuous
[1] "Remove cluster labels:" "CD86 MUTATED"          
clus
  CD86 MUTATED CD86 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-YY-A8LH 
"CD86 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CD86 MUTATED    4  2  0  0
  CD86 WILD-TYPE 73 46  1  3
D41V11, multiclass
    clus
vv   CD86 MUTATED CD86 WILD-TYPE
  R0            4             73
  R1            2             46
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD86 MUTATED       1                         0     5
  CD86 WILD-TYPE     1                         5   120
D41V13, multiclass
                           clus
vv                          CD86 MUTATED CD86 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                cls
clus              0  1
  CD86 MUTATED    0  6
  CD86 WILD-TYPE  3 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      0    6
  CD86 WILD-TYPE    3   98
                        clus
vv                       CD86 MUTATED CD86 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6             98
[1] 2 2
[1] FALSE

Clustering(42) Variable = RNF32 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2              0  1
  RNF32 MUTATED    0  4
  RNF32 WILD-TYPE 62 68
  RNF32 MUTATED RNF32 WILD-TYPE 
              4             130 
  RNF32 MUTATED RNF32 WILD-TYPE 
              4              68 
$`RNF32 MUTATED`
TCGA-HZ-7925 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-IB-7651 
       20.19        12.03         3.95        19.82 

$`RNF32 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       23.21         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  RNF32 MUTATED RNF32 WILD-TYPE 
           3.95            0.13 
  RNF32 MUTATED RNF32 WILD-TYPE 
          20.19           75.12 
  RNF32 MUTATED RNF32 WILD-TYPE 
         15.925          13.745 
[1] "4.0 - 20.2 (15.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.2"
D42V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RNF32 MUTATED          0        0         0         4         0        0
  RNF32 WILD-TYPE        4        6        20        95         4        3
D42V3, multiclass
           clus
vv          RNF32 MUTATED RNF32 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RNF32 MUTATED     0   0     4
  RNF32 WILD-TYPE   5  13   114
D42V4, multiclass
       clus
vv      RNF32 MUTATED RNF32 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                 cls
clus                0   1
  RNF32 MUTATED     0   4
  RNF32 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      0    4
  RNF32 WILD-TYPE   32  100
   clus
vv  RNF32 MUTATED RNF32 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D42V6, binary
                 cls
clus               0  1
  RNF32 MUTATED    1  0
  RNF32 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      1    0
  RNF32 WILD-TYPE   61    3
   clus
vv  RNF32 MUTATED RNF32 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus               0  1
  RNF32 MUTATED    1  3
  RNF32 WILD-TYPE 61 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      1    3
  RNF32 WILD-TYPE   61   71
        clus
vv       RNF32 MUTATED RNF32 WILD-TYPE
  FEMALE             1              61
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF32 MUTATED                                     4
  RNF32 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF32 MUTATED                                       0
  RNF32 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF32 MUTATED                                                  0
  RNF32 WILD-TYPE                                                2
D42V8, multiclass
                                                  clus
vv                                                 RNF32 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RNF32 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, continuous
[1] "Remove cluster labels:" "RNF32 MUTATED"         
clus
  RNF32 MUTATED RNF32 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
D42V10, continuous
[1] "Remove cluster labels:" "RNF32 MUTATED"         
clus
  RNF32 MUTATED RNF32 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RNF32 MUTATED    3  1  0  0
  RNF32 WILD-TYPE 74 47  1  3
D42V11, multiclass
    clus
vv   RNF32 MUTATED RNF32 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF32 MUTATED       0                         0     4
  RNF32 WILD-TYPE     2                         5   121
D42V13, multiclass
                           clus
vv                          RNF32 MUTATED RNF32 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                 cls
clus                0   1
  RNF32 MUTATED     0   4
  RNF32 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      0    4
  RNF32 WILD-TYPE    3  100
                        clus
vv                       RNF32 MUTATED RNF32 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(43) Variable = SDCBP MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  SDCBP MUTATED    2  4
  SDCBP WILD-TYPE 60 68
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             128 
  SDCBP MUTATED SDCBP WILD-TYPE 
              4              68 
$`SDCBP MUTATED`
TCGA-HZ-7926 TCGA-HZ-8005 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7889 TCGA-RB-AA9M 
       17.03         3.95        15.35        41.33        15.81         9.40 

$`SDCBP WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        19.82        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       43.79        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  SDCBP MUTATED SDCBP WILD-TYPE 
           3.95            0.13 
  SDCBP MUTATED SDCBP WILD-TYPE 
          41.33           75.12 
  SDCBP MUTATED SDCBP WILD-TYPE 
          15.58           13.50 
[1] "4.0 - 41.3 (15.6)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.2"
D43V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SDCBP MUTATED          0        0         0         6         0        0
  SDCBP WILD-TYPE        4        6        20        93         4        3
D43V3, multiclass
           clus
vv          SDCBP MUTATED SDCBP WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             6              93
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SDCBP MUTATED     1   0     5
  SDCBP WILD-TYPE   4  13   113
D43V4, multiclass
       clus
vv      SDCBP MUTATED SDCBP WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                 cls
clus               0  1
  SDCBP MUTATED    0  6
  SDCBP WILD-TYPE 32 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      0    6
  SDCBP WILD-TYPE   32   98
   clus
vv  SDCBP MUTATED SDCBP WILD-TYPE
  0             0              32
  1             6              98
[1] 2 2
[1] FALSE
D43V6, binary
                 cls
clus               0  1
  SDCBP MUTATED    3  0
  SDCBP WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      3    0
  SDCBP WILD-TYPE   59    3
   clus
vv  SDCBP MUTATED SDCBP WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus               0  1
  SDCBP MUTATED    3  3
  SDCBP WILD-TYPE 59 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      3    3
  SDCBP WILD-TYPE   59   71
        clus
vv       SDCBP MUTATED SDCBP WILD-TYPE
  FEMALE             3              59
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SDCBP MUTATED                                     6
  SDCBP WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SDCBP MUTATED                                       0
  SDCBP WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SDCBP MUTATED                                                  0
  SDCBP WILD-TYPE                                                2
D43V8, multiclass
                                                  clus
vv                                                 SDCBP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SDCBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, continuous
[1] "Remove cluster labels:" "SDCBP MUTATED"         
clus
  SDCBP MUTATED SDCBP WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
D43V10, continuous
[1] "Remove cluster labels:" "SDCBP MUTATED"         
clus
  SDCBP MUTATED SDCBP WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7651      TCGA-IB-7886      TCGA-IB-7891 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-YY-A8LH 
"SDCBP WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SDCBP MUTATED    3  2  0  1
  SDCBP WILD-TYPE 74 46  1  2
D43V11, multiclass
    clus
vv   SDCBP MUTATED SDCBP WILD-TYPE
  R0             3              74
  R1             2              46
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SDCBP MUTATED       0                         1     4
  SDCBP WILD-TYPE     2                         4   121
D43V13, multiclass
                           clus
vv                          SDCBP MUTATED SDCBP WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                 cls
clus               0  1
  SDCBP MUTATED    0  5
  SDCBP WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      0    5
  SDCBP WILD-TYPE    3   99
                        clus
vv                       SDCBP MUTATED SDCBP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(44) Variable = CDC27 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    3  4
  CDC27 WILD-TYPE 59 68
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             127 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              68 
$`CDC27 MUTATED`
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-FB-AAPY TCGA-HZ-7926 TCGA-IB-AAUP TCGA-LB-A8F3 
       23.61        20.84        34.82        17.03        14.17        12.46 
TCGA-XD-AAUI 
       12.03 

$`CDC27 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
        9.60        53.00         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       24.07        14.76        12.43         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       19.50         0.13        20.19        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        8.05        12.92        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  CDC27 MUTATED CDC27 WILD-TYPE 
          12.03            0.13 
  CDC27 MUTATED CDC27 WILD-TYPE 
          34.82           75.12 
  CDC27 MUTATED CDC27 WILD-TYPE 
          17.03           13.32 
[1] "12.0 - 34.8 (17.0)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.3"
D44V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CDC27 MUTATED          0        0         2         5         0        0
  CDC27 WILD-TYPE        4        6        18        94         4        3
D44V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CDC27 MUTATED     0   1     6
  CDC27 WILD-TYPE   5  12   112
D44V4, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             6             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  5
  CDC27 WILD-TYPE 30 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    5
  CDC27 WILD-TYPE   30   99
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             2              30
  1             5              99
[1] 2 2
[1] FALSE
D44V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    1  0
  CDC27 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    0
  CDC27 WILD-TYPE   61    3
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  5
  CDC27 WILD-TYPE 60 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    5
  CDC27 WILD-TYPE   60   69
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             2              60
  MALE               5              69
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC27 MUTATED                                     7
  CDC27 WILD-TYPE                                 115
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC27 MUTATED                                       0
  CDC27 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC27 MUTATED                                                  0
  CDC27 WILD-TYPE                                                2
D44V8, multiclass
                                                  clus
vv                                                 CDC27 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CDC27 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q      TCGA-HZ-A8P0 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
D44V10, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-H6-8124 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUL 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-YY-A8LH 
"CDC27 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CDC27 MUTATED    4  2  0  1
  CDC27 WILD-TYPE 73 46  1  2
D44V11, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0             4              73
  R1             2              46
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         3     4
  CDC27 WILD-TYPE     2                         2   121
D44V13, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             3               2
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                 cls
clus               0  1
  CDC27 MUTATED    0  7
  CDC27 WILD-TYPE  3 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    7
  CDC27 WILD-TYPE    3   97
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7              97
[1] 2 2
[1] FALSE

Clustering(45) Variable = NLRP2 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2              0  1
  NLRP2 MUTATED    1  4
  NLRP2 WILD-TYPE 61 68
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              5             129 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              4              68 
$`NLRP2 MUTATED`
TCGA-F2-A44G TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-8127 TCGA-OE-A75W 
        7.66        10.13        19.82        17.16         8.78 

$`NLRP2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74        10.98        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        21.70        16.14         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  NLRP2 MUTATED NLRP2 WILD-TYPE 
           7.66            0.13 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
          19.82           75.12 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
          10.13           13.81 
[1] "7.7 - 19.8 (10.1)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.1"
D45V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NLRP2 MUTATED          0        0         1         4         0        0
  NLRP2 WILD-TYPE        4        6        19        95         4        3
D45V3, multiclass
           clus
vv          NLRP2 MUTATED NLRP2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NLRP2 MUTATED     0   0     5
  NLRP2 WILD-TYPE   5  13   113
D45V4, multiclass
       clus
vv      NLRP2 MUTATED NLRP2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                 cls
clus                0   1
  NLRP2 MUTATED     1   4
  NLRP2 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      1    4
  NLRP2 WILD-TYPE   31  100
   clus
vv  NLRP2 MUTATED NLRP2 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D45V6, binary
                 cls
clus               0  1
  NLRP2 MUTATED    4  0
  NLRP2 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      4    0
  NLRP2 WILD-TYPE   58    3
   clus
vv  NLRP2 MUTATED NLRP2 WILD-TYPE
  0             4              58
  1             0               3
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus               0  1
  NLRP2 MUTATED    2  3
  NLRP2 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      2    3
  NLRP2 WILD-TYPE   60   71
        clus
vv       NLRP2 MUTATED NLRP2 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NLRP2 MUTATED                                     5
  NLRP2 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NLRP2 MUTATED                                       0
  NLRP2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NLRP2 MUTATED                                                  0
  NLRP2 WILD-TYPE                                                2
D45V8, multiclass
                                                  clus
vv                                                 NLRP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NLRP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, continuous
D45V10, continuous
                 vv
clus              R0 R1 R2 RX
  NLRP2 MUTATED    2  3  0  0
  NLRP2 WILD-TYPE 75 45  1  3
D45V11, multiclass
    clus
vv   NLRP2 MUTATED NLRP2 WILD-TYPE
  R0             2              75
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP2 MUTATED       0                         0     5
  NLRP2 WILD-TYPE     2                         5   120
D45V13, multiclass
                           clus
vv                          NLRP2 MUTATED NLRP2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                 cls
clus               0  1
  NLRP2 MUTATED    0  5
  NLRP2 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      0    5
  NLRP2 WILD-TYPE    3   99
                        clus
vv                       NLRP2 MUTATED NLRP2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(46) Variable = PLIN4 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2              0  1
  PLIN4 MUTATED    1  5
  PLIN4 WILD-TYPE 61 67
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              6             128 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              5              67 
$`PLIN4 MUTATED`
TCGA-FB-AAPY TCGA-HZ-7926 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-A5SQ TCGA-RB-AA9M 
       34.82        17.03        12.95        19.82         7.20         9.40 

$`PLIN4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        12.00        15.85        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  PLIN4 MUTATED PLIN4 WILD-TYPE 
           7.20            0.13 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
          34.82           75.12 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
         14.990          13.745 
[1] "7.2 - 34.8 (15.0)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.5"
D46V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PLIN4 MUTATED          0        1         0         4         0        1
  PLIN4 WILD-TYPE        4        5        20        95         4        2
D46V3, multiclass
           clus
vv          PLIN4 MUTATED PLIN4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PLIN4 MUTATED     1   2     3
  PLIN4 WILD-TYPE   4  11   115
D46V4, multiclass
       clus
vv      PLIN4 MUTATED PLIN4 WILD-TYPE
  T1                1               4
  T2                2              11
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                 cls
clus               0  1
  PLIN4 MUTATED    1  5
  PLIN4 WILD-TYPE 31 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      1    5
  PLIN4 WILD-TYPE   31   99
   clus
vv  PLIN4 MUTATED PLIN4 WILD-TYPE
  0             1              31
  1             5              99
[1] 2 2
[1] FALSE
D46V6, binary
                 cls
clus               0  1
  PLIN4 MUTATED    2  1
  PLIN4 WILD-TYPE 60  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      2    1
  PLIN4 WILD-TYPE   60    2
   clus
vv  PLIN4 MUTATED PLIN4 WILD-TYPE
  0             2              60
  1             1               2
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus               0  1
  PLIN4 MUTATED    3  3
  PLIN4 WILD-TYPE 59 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      3    3
  PLIN4 WILD-TYPE   59   71
        clus
vv       PLIN4 MUTATED PLIN4 WILD-TYPE
  FEMALE             3              59
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLIN4 MUTATED                                     6
  PLIN4 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLIN4 MUTATED                                       0
  PLIN4 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLIN4 MUTATED                                                  0
  PLIN4 WILD-TYPE                                                2
D46V8, multiclass
                                                  clus
vv                                                 PLIN4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PLIN4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, continuous
D46V10, continuous
                 vv
clus              R0 R1 R2 RX
  PLIN4 MUTATED    4  1  0  1
  PLIN4 WILD-TYPE 73 47  1  2
D46V11, multiclass
    clus
vv   PLIN4 MUTATED PLIN4 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLIN4 MUTATED       0                         1     5
  PLIN4 WILD-TYPE     2                         4   120
D46V13, multiclass
                           clus
vv                          PLIN4 MUTATED PLIN4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                 cls
clus               0  1
  PLIN4 MUTATED    0  6
  PLIN4 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      0    6
  PLIN4 WILD-TYPE    3   98
                        clus
vv                       PLIN4 MUTATED PLIN4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(47) Variable = CBX3 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2             0  1
  CBX3 MUTATED    1  2
  CBX3 WILD-TYPE 61 70
  CBX3 MUTATED CBX3 WILD-TYPE 
             3            131 
  CBX3 MUTATED CBX3 WILD-TYPE 
             2             70 
$`CBX3 MUTATED`
TCGA-2L-AAQI TCGA-FB-AAPU TCGA-H6-8124 
        3.39        12.53        12.89 

$`CBX3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43         7.50        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03         1.02        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CBX3 MUTATED CBX3 WILD-TYPE 
          3.39           0.13 
  CBX3 MUTATED CBX3 WILD-TYPE 
         12.89          75.12 
  CBX3 MUTATED CBX3 WILD-TYPE 
         12.53          13.84 
[1] "3.4 - 12.9 (12.5)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.7"
D47V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CBX3 MUTATED          0        0         1         2         0        0
  CBX3 WILD-TYPE        4        6        19        97         4        3
D47V3, multiclass
           clus
vv          CBX3 MUTATED CBX3 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            2             97
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  CBX3 MUTATED     0   0     3
  CBX3 WILD-TYPE   5  13   115
D47V4, multiclass
       clus
vv      CBX3 MUTATED CBX3 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                cls
clus               0   1
  CBX3 MUTATED     1   2
  CBX3 WILD-TYPE  31 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      1    2
  CBX3 WILD-TYPE   31  102
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            1             31
  1            2            102
[1] 2 2
[1] FALSE
D47V6, binary
                cls
clus              0  1
  CBX3 MUTATED    1  0
  CBX3 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      1    0
  CBX3 WILD-TYPE   61    3
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D47V7, binary
                cls
clus              0  1
  CBX3 MUTATED    2  1
  CBX3 WILD-TYPE 60 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      2    1
  CBX3 WILD-TYPE   60   73
        clus
vv       CBX3 MUTATED CBX3 WILD-TYPE
  FEMALE            2             60
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CBX3 MUTATED                                     3
  CBX3 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CBX3 MUTATED                                       0
  CBX3 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CBX3 MUTATED                                                  0
  CBX3 WILD-TYPE                                                2
D47V8, multiclass
                                                  clus
vv                                                 CBX3 MUTATED CBX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, continuous
[1] "Remove cluster labels:" "CBX3 MUTATED"          
clus
  CBX3 MUTATED CBX3 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-A45N     TCGA-HZ-A77Q 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
D47V10, continuous
[1] "Remove cluster labels:" "CBX3 MUTATED"          
clus
  CBX3 MUTATED CBX3 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CBX3 MUTATED    1  2  0  0
  CBX3 WILD-TYPE 76 46  1  3
D47V11, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  R0            1             76
  R1            2             46
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBX3 MUTATED       1                         0     2
  CBX3 WILD-TYPE     1                         5   123
D47V13, multiclass
                           clus
vv                          CBX3 MUTATED CBX3 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                cls
clus               0   1
  CBX3 MUTATED     0   2
  CBX3 WILD-TYPE   3 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      0    2
  CBX3 WILD-TYPE    3  102
                        clus
vv                       CBX3 MUTATED CBX3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            2            102
[1] 2 2
[1] FALSE

Clustering(48) Variable = SUZ12 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2              0  1
  SUZ12 MUTATED    1  3
  SUZ12 WILD-TYPE 61 69
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             130 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3              69 
$`SUZ12 MUTATED`
TCGA-F2-6879 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       10.98        20.19        19.82        41.33 

$`SUZ12 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  SUZ12 MUTATED SUZ12 WILD-TYPE 
          10.98            0.13 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
          41.33           75.12 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
         20.005          13.500 
[1] "11.0 - 41.3 (20.0)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.1"
D48V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SUZ12 MUTATED          0        0         0         4         0        0
  SUZ12 WILD-TYPE        4        6        20        95         4        3
D48V3, multiclass
           clus
vv          SUZ12 MUTATED SUZ12 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SUZ12 MUTATED     0   0     4
  SUZ12 WILD-TYPE   5  13   114
D48V4, multiclass
       clus
vv      SUZ12 MUTATED SUZ12 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   4
  SUZ12 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    4
  SUZ12 WILD-TYPE   32  100
   clus
vv  SUZ12 MUTATED SUZ12 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D48V6, binary
                 cls
clus               0  1
  SUZ12 MUTATED    3  0
  SUZ12 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      3    0
  SUZ12 WILD-TYPE   59    3
   clus
vv  SUZ12 MUTATED SUZ12 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus               0  1
  SUZ12 MUTATED    2  2
  SUZ12 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      2    2
  SUZ12 WILD-TYPE   60   72
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SUZ12 MUTATED                                     3
  SUZ12 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SUZ12 MUTATED                                       1
  SUZ12 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SUZ12 MUTATED                                                  0
  SUZ12 WILD-TYPE                                                2
D48V8, multiclass
                                                  clus
vv                                                 SUZ12 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SUZ12 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, continuous
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
D48V10, continuous
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7891 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-YY-A8LH 
"SUZ12 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SUZ12 MUTATED    4  0  0  0
  SUZ12 WILD-TYPE 73 48  1  3
D48V11, multiclass
    clus
vv   SUZ12 MUTATED SUZ12 WILD-TYPE
  R0             4              73
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SUZ12 MUTATED       0                         0     4
  SUZ12 WILD-TYPE     2                         5   121
D48V13, multiclass
                           clus
vv                          SUZ12 MUTATED SUZ12 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   3
  SUZ12 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    3
  SUZ12 WILD-TYPE    3  101
                        clus
vv                       SUZ12 MUTATED SUZ12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(49) Variable = MTBP MUTATION ANALYSIS
D49V1, survival
                sevent
clus2             0  1
  MTBP MUTATED    1  2
  MTBP WILD-TYPE 61 70
  MTBP MUTATED MTBP WILD-TYPE 
             3            131 
  MTBP MUTATED MTBP WILD-TYPE 
             2             70 
$`MTBP MUTATED`
TCGA-IB-7649 TCGA-IB-7887 TCGA-IB-AAUS 
       15.35         3.62         7.40 

$`MTBP WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         4.04        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  MTBP MUTATED MTBP WILD-TYPE 
          3.62           0.13 
  MTBP MUTATED MTBP WILD-TYPE 
         15.35          75.12 
  MTBP MUTATED MTBP WILD-TYPE 
          7.40          13.81 
[1] "3.6 - 15.3 (7.4)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.8"
D49V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MTBP MUTATED          0        0         0         3         0        0
  MTBP WILD-TYPE        4        6        20        96         4        3
D49V3, multiclass
           clus
vv          MTBP MUTATED MTBP WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  MTBP MUTATED     0   0     3
  MTBP WILD-TYPE   5  13   115
D49V4, multiclass
       clus
vv      MTBP MUTATED MTBP WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                cls
clus               0   1
  MTBP MUTATED     0   3
  MTBP WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      0    3
  MTBP WILD-TYPE   32  101
   clus
vv  MTBP MUTATED MTBP WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D49V6, binary
                cls
clus              0  1
  MTBP MUTATED    3  0
  MTBP WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      3    0
  MTBP WILD-TYPE   59    3
   clus
vv  MTBP MUTATED MTBP WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus              0  1
  MTBP MUTATED    3  0
  MTBP WILD-TYPE 59 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      3    0
  MTBP WILD-TYPE   59   74
        clus
vv       MTBP MUTATED MTBP WILD-TYPE
  FEMALE            3             59
  MALE              0             74
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MTBP MUTATED                                     3
  MTBP WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MTBP MUTATED                                       0
  MTBP WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MTBP MUTATED                                                  0
  MTBP WILD-TYPE                                                2
D49V8, multiclass
                                                  clus
vv                                                 MTBP MUTATED MTBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, continuous
D49V10, continuous
[1] "Remove cluster labels:" "MTBP MUTATED"          
clus
  MTBP MUTATED MTBP WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-YY-A8LH 
"MTBP WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MTBP MUTATED    0  3  0  0
  MTBP WILD-TYPE 77 45  1  3
D49V11, multiclass
    clus
vv   MTBP MUTATED MTBP WILD-TYPE
  R0            0             77
  R1            3             45
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTBP MUTATED       0                         0     2
  MTBP WILD-TYPE     2                         5   123
D49V13, multiclass
[1] "Remove cluster labels:" "MTBP MUTATED"          
clus
  MTBP MUTATED MTBP WILD-TYPE 
             2            130 
    TCGA-2J-AAB1     TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-2J-AAB9     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-2J-AABH     TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABR 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-2J-AABU     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-2L-AAQI     TCGA-2L-AAQJ     TCGA-2L-AAQL     TCGA-3A-A9I5 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-3A-A9I7     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IC 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-3A-A9IH     TCGA-3A-A9IU     TCGA-3A-A9IX     TCGA-3A-A9IZ 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-3A-A9J0     TCGA-3E-AAAY     TCGA-3E-AAAZ     TCGA-F2-6879 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-F2-A44G     TCGA-F2-A44H     TCGA-F2-A7TX     TCGA-F2-A8YN 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A545     TCGA-FB-A5VM 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPU     TCGA-FB-AAPY 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-FB-AAPZ     TCGA-FB-AAQ0     TCGA-FB-AAQ1     TCGA-FB-AAQ2 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-FB-AAQ3     TCGA-H6-8124     TCGA-H6-A45N     TCGA-HZ-7919 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-7922     TCGA-HZ-7925     TCGA-HZ-7926     TCGA-HZ-8001 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-8002     TCGA-HZ-8003     TCGA-HZ-8005     TCGA-HZ-8315 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-8317     TCGA-HZ-8519     TCGA-HZ-8636     TCGA-HZ-8637 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A49G     TCGA-HZ-A49H     TCGA-HZ-A49I     TCGA-HZ-A4BH 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A4BK     TCGA-HZ-A77O     TCGA-HZ-A77P     TCGA-HZ-A77Q 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7646 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-7647     TCGA-IB-7651     TCGA-IB-7652     TCGA-IB-7885 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-7886     TCGA-IB-7888     TCGA-IB-7889     TCGA-IB-7891 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-7893     TCGA-IB-7897     TCGA-IB-8126     TCGA-IB-8127 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-A5SO     TCGA-IB-A5SP     TCGA-IB-A5SQ     TCGA-IB-A5SS 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-A5ST     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7LX 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUM     TCGA-IB-AAUN     TCGA-IB-AAUO 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-AAUP     TCGA-IB-AAUQ     TCGA-IB-AAUR     TCGA-IB-AAUT 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A8F3     TCGA-LB-A9Q5 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-OE-A75W     TCGA-PZ-A5RE     TCGA-Q3-A5QY     TCGA-Q3-AA2A 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-RB-A7B8     TCGA-RB-AA9M     TCGA-S4-A8RM     TCGA-S4-A8RO 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-US-A776     TCGA-US-A779 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-US-A77E     TCGA-US-A77G     TCGA-XD-AAUG     TCGA-XD-AAUH 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XD-AAUL     TCGA-YB-A89D     TCGA-YH-A8SY 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-YY-A8LH     TCGA-Z5-AAPL 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" 
D49V14, binary
                cls
clus               0   1
  MTBP MUTATED     0   2
  MTBP WILD-TYPE   3 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      0    2
  MTBP WILD-TYPE    3  102
                        clus
vv                       MTBP MUTATED MTBP WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            2            102
[1] 2 2
[1] FALSE

Clustering(50) Variable = SYT14 MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2              0  1
  SYT14 MUTATED    0  4
  SYT14 WILD-TYPE 62 68
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             130 
  SYT14 MUTATED SYT14 WILD-TYPE 
              4              68 
$`SYT14 MUTATED`
TCGA-F2-6879 TCGA-HZ-8005 TCGA-IB-7651 TCGA-IB-7887 
       10.98         3.95        19.82         3.62 

$`SYT14 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  SYT14 MUTATED SYT14 WILD-TYPE 
           3.62            0.13 
  SYT14 MUTATED SYT14 WILD-TYPE 
          19.82           75.12 
  SYT14 MUTATED SYT14 WILD-TYPE 
          7.465          13.825 
[1] "3.6 - 19.8 (7.5)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.7"
D50V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SYT14 MUTATED          0        0         0         4         0        0
  SYT14 WILD-TYPE        4        6        20        95         4        3
D50V3, multiclass
           clus
vv          SYT14 MUTATED SYT14 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SYT14 MUTATED     0   0     4
  SYT14 WILD-TYPE   5  13   114
D50V4, multiclass
       clus
vv      SYT14 MUTATED SYT14 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                 cls
clus                0   1
  SYT14 MUTATED     0   4
  SYT14 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      0    4
  SYT14 WILD-TYPE   32  100
   clus
vv  SYT14 MUTATED SYT14 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D50V6, binary
                 cls
clus               0  1
  SYT14 MUTATED    3  0
  SYT14 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      3    0
  SYT14 WILD-TYPE   59    3
   clus
vv  SYT14 MUTATED SYT14 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D50V7, binary
                 cls
clus               0  1
  SYT14 MUTATED    2  2
  SYT14 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      2    2
  SYT14 WILD-TYPE   60   72
        clus
vv       SYT14 MUTATED SYT14 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYT14 MUTATED                                     3
  SYT14 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYT14 MUTATED                                       1
  SYT14 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYT14 MUTATED                                                  0
  SYT14 WILD-TYPE                                                2
D50V8, multiclass
                                                  clus
vv                                                 SYT14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SYT14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, continuous
[1] "Remove cluster labels:" "SYT14 MUTATED"         
clus
  SYT14 MUTATED SYT14 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
D50V10, continuous
[1] "Remove cluster labels:" "SYT14 MUTATED"         
clus
  SYT14 MUTATED SYT14 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SYT14 MUTATED    2  2  0  0
  SYT14 WILD-TYPE 75 46  1  3
D50V11, multiclass
    clus
vv   SYT14 MUTATED SYT14 WILD-TYPE
  R0             2              75
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYT14 MUTATED       0                         0     4
  SYT14 WILD-TYPE     2                         5   121
D50V13, multiclass
                           clus
vv                          SYT14 MUTATED SYT14 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                 cls
clus                0   1
  SYT14 MUTATED     0   3
  SYT14 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      0    3
  SYT14 WILD-TYPE    3  101
                        clus
vv                       SYT14 MUTATED SYT14 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(51) Variable = RNF43 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2              0  1
  RNF43 MUTATED    5  2
  RNF43 WILD-TYPE 57 70
  RNF43 MUTATED RNF43 WILD-TYPE 
              7             127 
  RNF43 MUTATED RNF43 WILD-TYPE 
              2              70 
$`RNF43 MUTATED`
TCGA-2J-AABE TCGA-3E-AAAZ TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-8127 TCGA-S4-A8RM 
       22.22        71.74         1.08        19.82        17.16        21.24 
TCGA-YY-A8LH 
       66.28 

$`RNF43 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        12.39        75.12        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32         9.40        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-Z5-AAPL 
        0.69 

  RNF43 MUTATED RNF43 WILD-TYPE 
           1.08            0.13 
  RNF43 MUTATED RNF43 WILD-TYPE 
          71.74           75.12 
  RNF43 MUTATED RNF43 WILD-TYPE 
          21.24           12.99 
[1] "1.1 - 71.7 (21.2)" "0.1 - 75.1 (13.0)"
[1] "hr=" "4.1"
D51V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RNF43 MUTATED          0        0         2         5         0        0
  RNF43 WILD-TYPE        4        6        18        94         4        3
D51V3, multiclass
           clus
vv          RNF43 MUTATED RNF43 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RNF43 MUTATED     0   0     7
  RNF43 WILD-TYPE   5  13   111
D51V4, multiclass
       clus
vv      RNF43 MUTATED RNF43 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             7             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                 cls
clus               0  1
  RNF43 MUTATED    2  5
  RNF43 WILD-TYPE 30 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      2    5
  RNF43 WILD-TYPE   30   99
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             2              30
  1             5              99
[1] 2 2
[1] FALSE
D51V6, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  0
  RNF43 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    0
  RNF43 WILD-TYPE   59    3
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  4
  RNF43 WILD-TYPE 59 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    4
  RNF43 WILD-TYPE   59   70
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE             3              59
  MALE               4              70
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF43 MUTATED                                     6
  RNF43 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF43 MUTATED                                       1
  RNF43 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF43 MUTATED                                                  0
  RNF43 WILD-TYPE                                                2
D51V8, multiclass
                                                  clus
vv                                                 RNF43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RNF43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, continuous
D51V10, continuous
                 vv
clus              R0 R1 R2 RX
  RNF43 MUTATED    5  1  0  0
  RNF43 WILD-TYPE 72 47  1  3
D51V11, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0             5              72
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED       0                         0     7
  RNF43 WILD-TYPE     2                         5   118
D51V13, multiclass
                           clus
vv                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                 cls
clus               0  1
  RNF43 MUTATED    1  5
  RNF43 WILD-TYPE  2 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      1    5
  RNF43 WILD-TYPE    2   99
                        clus
vv                       RNF43 MUTATED RNF43 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(52) Variable = AAK1 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2             0  1
  AAK1 MUTATED    0  4
  AAK1 WILD-TYPE 62 68
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            130 
  AAK1 MUTATED AAK1 WILD-TYPE 
             4             68 
$`AAK1 MUTATED`
TCGA-3A-A9IB TCGA-IB-7890 TCGA-IB-7897 TCGA-IB-A5SQ 
        7.36        19.66        15.98         7.20 

$`AAK1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 
       41.33         4.04         3.62        43.79        15.81        21.30 
TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
        3.85         2.47        17.16        12.00        15.85        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  AAK1 MUTATED AAK1 WILD-TYPE 
          7.20           0.13 
  AAK1 MUTATED AAK1 WILD-TYPE 
         19.66          75.12 
  AAK1 MUTATED AAK1 WILD-TYPE 
        11.670         13.745 
[1] "7.2 - 19.7 (11.7)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.6"
D52V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AAK1 MUTATED          0        2         0         2         0        0
  AAK1 WILD-TYPE        4        4        20        97         4        3
D52V3, multiclass
           clus
vv          AAK1 MUTATED AAK1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             2              4
  STAGE IIA            0             20
  STAGE IIB            2             97
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  AAK1 MUTATED     0   2     2
  AAK1 WILD-TYPE   5  11   116
D52V4, multiclass
       clus
vv      AAK1 MUTATED AAK1 WILD-TYPE
  T1               0              5
  T2               2             11
  T3+T4            2            116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                cls
clus               0   1
  AAK1 MUTATED     2   2
  AAK1 WILD-TYPE  30 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      2    2
  AAK1 WILD-TYPE   30  102
   clus
vv  AAK1 MUTATED AAK1 WILD-TYPE
  0            2             30
  1            2            102
[1] 2 2
[1] FALSE
D52V6, binary
                cls
clus              0  1
  AAK1 MUTATED    3  0
  AAK1 WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      3    0
  AAK1 WILD-TYPE   59    3
   clus
vv  AAK1 MUTATED AAK1 WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D52V7, binary
                cls
clus              0  1
  AAK1 MUTATED    3  1
  AAK1 WILD-TYPE 59 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      3    1
  AAK1 WILD-TYPE   59   73
        clus
vv       AAK1 MUTATED AAK1 WILD-TYPE
  FEMALE            3             59
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AAK1 MUTATED                                     4
  AAK1 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AAK1 MUTATED                                       0
  AAK1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AAK1 MUTATED                                                  0
  AAK1 WILD-TYPE                                                2
D52V8, multiclass
                                                  clus
vv                                                 AAK1 MUTATED AAK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, continuous
[1] "Remove cluster labels:" "AAK1 MUTATED"          
clus
  AAK1 MUTATED AAK1 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A4P5 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N     TCGA-HZ-A77Q 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
D52V10, continuous
[1] "Remove cluster labels:" "AAK1 MUTATED"          
clus
  AAK1 MUTATED AAK1 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  AAK1 MUTATED    4  0  0  0
  AAK1 WILD-TYPE 73 48  1  3
D52V11, multiclass
    clus
vv   AAK1 MUTATED AAK1 WILD-TYPE
  R0            4             73
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AAK1 MUTATED       0                         0     3
  AAK1 WILD-TYPE     2                         5   122
D52V13, multiclass
                           clus
vv                          AAK1 MUTATED AAK1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                cls
clus               0   1
  AAK1 MUTATED     0   3
  AAK1 WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      0    3
  AAK1 WILD-TYPE    3  101
                        clus
vv                       AAK1 MUTATED AAK1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(53) Variable = HSPE1 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2              0  1
  HSPE1 MUTATED    2  2
  HSPE1 WILD-TYPE 60 70
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             130 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              2              70 
$`HSPE1 MUTATED`
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-HZ-A4BH TCGA-HZ-A77P 
        7.36        24.26         6.38        10.85 

$`HSPE1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IH TCGA-3A-A9IU 
        9.60        53.00        23.61        20.84        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.92        21.70        16.14        10.13        21.60         5.26 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  HSPE1 MUTATED HSPE1 WILD-TYPE 
           6.38            0.13 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
          24.26           75.12 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
          9.105          13.825 
[1] "6.4 - 24.3 (9.1)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "1.1"
D53V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HSPE1 MUTATED          0        0         0         4         0        0
  HSPE1 WILD-TYPE        4        6        20        95         4        3
D53V3, multiclass
           clus
vv          HSPE1 MUTATED HSPE1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  HSPE1 MUTATED     0   0     4
  HSPE1 WILD-TYPE   5  13   114
D53V4, multiclass
       clus
vv      HSPE1 MUTATED HSPE1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                 cls
clus                0   1
  HSPE1 MUTATED     0   4
  HSPE1 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    4
  HSPE1 WILD-TYPE   32  100
   clus
vv  HSPE1 MUTATED HSPE1 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D53V6, binary
                 cls
clus               0  1
  HSPE1 MUTATED    0  0
  HSPE1 WILD-TYPE 62  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    0
  HSPE1 WILD-TYPE   62    3
D53V7, binary
                 cls
clus               0  1
  HSPE1 MUTATED    2  2
  HSPE1 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      2    2
  HSPE1 WILD-TYPE   60   72
        clus
vv       HSPE1 MUTATED HSPE1 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HSPE1 MUTATED                                     3
  HSPE1 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HSPE1 MUTATED                                       1
  HSPE1 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HSPE1 MUTATED                                                  0
  HSPE1 WILD-TYPE                                                2
D53V8, multiclass
                                                  clus
vv                                                 HSPE1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 HSPE1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, continuous
[1] "Remove cluster labels:" "HSPE1 MUTATED"         
clus
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
D53V10, continuous
[1] "Remove cluster labels:" "HSPE1 MUTATED"         
clus
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HSPE1 MUTATED    3  1  0  0
  HSPE1 WILD-TYPE 74 47  1  3
D53V11, multiclass
    clus
vv   HSPE1 MUTATED HSPE1 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSPE1 MUTATED       0                         0     4
  HSPE1 WILD-TYPE     2                         5   121
D53V13, multiclass
                           clus
vv                          HSPE1 MUTATED HSPE1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                 cls
clus                0   1
  HSPE1 MUTATED     0   3
  HSPE1 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    3
  HSPE1 WILD-TYPE    3  101
                        clus
vv                       HSPE1 MUTATED HSPE1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(54) Variable = TMCC1 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2              0  1
  TMCC1 MUTATED    2  5
  TMCC1 WILD-TYPE 60 67
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             127 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              5              67 
$`TMCC1 MUTATED`
TCGA-2J-AABV TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7651 
       21.44        23.61         7.36         5.26         1.08        19.82 
TCGA-IB-7890 
       19.66 

$`TMCC1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       53.00        20.84        24.26        28.73        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        12.39        75.12        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P 
       21.70        16.14        10.13         6.38        21.60        10.85 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  TMCC1 MUTATED TMCC1 WILD-TYPE 
           1.08            0.13 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          23.61           75.12 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          19.66           13.68 
[1] "1.1 - 23.6 (19.7)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D54V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TMCC1 MUTATED          0        1         0         6         0        0
  TMCC1 WILD-TYPE        4        5        20        93         4        3
D54V3, multiclass
           clus
vv          TMCC1 MUTATED TMCC1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             0              20
  STAGE IIB             6              93
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TMCC1 MUTATED     0   2     5
  TMCC1 WILD-TYPE   5  11   113
D54V4, multiclass
       clus
vv      TMCC1 MUTATED TMCC1 WILD-TYPE
  T1                0               5
  T2                2              11
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                 cls
clus               0  1
  TMCC1 MUTATED    1  6
  TMCC1 WILD-TYPE 31 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      1    6
  TMCC1 WILD-TYPE   31   98
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             1              31
  1             6              98
[1] 2 2
[1] FALSE
D54V6, binary
                 cls
clus               0  1
  TMCC1 MUTATED    3  0
  TMCC1 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      3    0
  TMCC1 WILD-TYPE   59    3
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus               0  1
  TMCC1 MUTATED    4  3
  TMCC1 WILD-TYPE 58 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      4    3
  TMCC1 WILD-TYPE   58   71
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  FEMALE             4              58
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMCC1 MUTATED                                     6
  TMCC1 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMCC1 MUTATED                                       1
  TMCC1 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMCC1 MUTATED                                                  0
  TMCC1 WILD-TYPE                                                2
D54V8, multiclass
                                                  clus
vv                                                 TMCC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TMCC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, continuous
D54V10, continuous
                 vv
clus              R0 R1 R2 RX
  TMCC1 MUTATED    6  1  0  0
  TMCC1 WILD-TYPE 71 47  1  3
D54V11, multiclass
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  R0             6              71
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCC1 MUTATED       0                         1     5
  TMCC1 WILD-TYPE     2                         4   120
D54V13, multiclass
                           clus
vv                          TMCC1 MUTATED TMCC1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                 cls
clus               0  1
  TMCC1 MUTATED    0  5
  TMCC1 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      0    5
  TMCC1 WILD-TYPE    3   99
                        clus
vv                       TMCC1 MUTATED TMCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(55) Variable = CFTR MUTATION ANALYSIS
D55V1, survival
                sevent
clus2             0  1
  CFTR MUTATED    2  5
  CFTR WILD-TYPE 60 67
  CFTR MUTATED CFTR WILD-TYPE 
             7            127 
  CFTR MUTATED CFTR WILD-TYPE 
             5             67 
$`CFTR MUTATED`
TCGA-3A-A9I5 TCGA-3E-AAAZ TCGA-HZ-8317 TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-7893 
       53.00        71.74        12.43        19.82        43.79         3.85 
TCGA-YB-A89D 
       11.51 

$`CFTR WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        12.39        75.12        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         3.95         9.83        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       15.81        19.66        21.30        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  CFTR MUTATED CFTR WILD-TYPE 
          3.85           0.13 
  CFTR MUTATED CFTR WILD-TYPE 
         71.74          75.12 
  CFTR MUTATED CFTR WILD-TYPE 
         19.82          13.68 
[1] "3.9 - 71.7 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.5"
D55V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CFTR MUTATED          1        0         3         3         0        0
  CFTR WILD-TYPE        3        6        17        96         4        3
D55V3, multiclass
           clus
vv          CFTR MUTATED CFTR WILD-TYPE
  STAGE IA             1              3
  STAGE IB             0              6
  STAGE IIA            3             17
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  CFTR MUTATED     1   0     6
  CFTR WILD-TYPE   4  13   112
D55V4, multiclass
       clus
vv      CFTR MUTATED CFTR WILD-TYPE
  T1               1              4
  T2               0             13
  T3+T4            6            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                cls
clus               0   1
  CFTR MUTATED     4   3
  CFTR WILD-TYPE  28 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      4    3
  CFTR WILD-TYPE   28  101
   clus
vv  CFTR MUTATED CFTR WILD-TYPE
  0            4             28
  1            3            101
[1] 2 2
[1] FALSE
D55V6, binary
                cls
clus              0  1
  CFTR MUTATED    3  0
  CFTR WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      3    0
  CFTR WILD-TYPE   59    3
   clus
vv  CFTR MUTATED CFTR WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D55V7, binary
                cls
clus              0  1
  CFTR MUTATED    3  4
  CFTR WILD-TYPE 59 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      3    4
  CFTR WILD-TYPE   59   70
        clus
vv       CFTR MUTATED CFTR WILD-TYPE
  FEMALE            3             59
  MALE              4             70
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CFTR MUTATED                                     7
  CFTR WILD-TYPE                                 115
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CFTR MUTATED                                       0
  CFTR WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CFTR MUTATED                                                  0
  CFTR WILD-TYPE                                                2
D55V8, multiclass
                                                  clus
vv                                                 CFTR MUTATED CFTR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7            115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, continuous
[1] "Remove cluster labels:" "CFTR MUTATED"          
clus
  CFTR MUTATED CFTR WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
D55V10, continuous
[1] "Remove cluster labels:" "CFTR MUTATED"          
clus
  CFTR MUTATED CFTR WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CFTR MUTATED    5  1  0  0
  CFTR WILD-TYPE 72 47  1  3
D55V11, multiclass
    clus
vv   CFTR MUTATED CFTR WILD-TYPE
  R0            5             72
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CFTR MUTATED       0                         1     6
  CFTR WILD-TYPE     2                         4   119
D55V13, multiclass
                           clus
vv                          CFTR MUTATED CFTR WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                cls
clus              0  1
  CFTR MUTATED    1  6
  CFTR WILD-TYPE  2 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      1    6
  CFTR WILD-TYPE    2   98
                        clus
vv                       CFTR MUTATED CFTR WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            6             98
[1] 2 2
[1] FALSE

Clustering(56) Variable = NAA20 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  NAA20 MUTATED    1  2
  NAA20 WILD-TYPE 61 70
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             131 
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              70 
$`NAA20 MUTATED`
TCGA-HZ-7925 TCGA-IB-7649 TCGA-IB-7885 
       20.19        15.35        41.33 

$`NAA20 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 
       49.38         4.77        21.90        19.82        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  NAA20 MUTATED NAA20 WILD-TYPE 
          15.35            0.13 
  NAA20 MUTATED NAA20 WILD-TYPE 
          41.33           75.12 
  NAA20 MUTATED NAA20 WILD-TYPE 
          20.19           13.32 
[1] "15.3 - 41.3 (20.2)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.4"
D56V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NAA20 MUTATED          0        0         0         3         0        0
  NAA20 WILD-TYPE        4        6        20        96         4        3
D56V3, multiclass
           clus
vv          NAA20 MUTATED NAA20 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NAA20 MUTATED     0   0     3
  NAA20 WILD-TYPE   5  13   115
D56V4, multiclass
       clus
vv      NAA20 MUTATED NAA20 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                 cls
clus                0   1
  NAA20 MUTATED     0   3
  NAA20 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      0    3
  NAA20 WILD-TYPE   32  101
   clus
vv  NAA20 MUTATED NAA20 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D56V6, binary
                 cls
clus               0  1
  NAA20 MUTATED    2  0
  NAA20 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      2    0
  NAA20 WILD-TYPE   60    3
   clus
vv  NAA20 MUTATED NAA20 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus               0  1
  NAA20 MUTATED    2  1
  NAA20 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      2    1
  NAA20 WILD-TYPE   60   73
        clus
vv       NAA20 MUTATED NAA20 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAA20 MUTATED                                     3
  NAA20 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAA20 MUTATED                                       0
  NAA20 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAA20 MUTATED                                                  0
  NAA20 WILD-TYPE                                                2
D56V8, multiclass
                                                  clus
vv                                                 NAA20 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NAA20 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, continuous
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
D56V10, continuous
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7651      TCGA-IB-7886      TCGA-IB-7891 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-YY-A8LH 
"NAA20 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NAA20 MUTATED    2  1  0  0
  NAA20 WILD-TYPE 75 47  1  3
D56V11, multiclass
    clus
vv   NAA20 MUTATED NAA20 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA20 MUTATED       0                         0     2
  NAA20 WILD-TYPE     2                         5   123
D56V13, multiclass
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2             130 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-2J-AAB9      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-2J-AABH      TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-2J-AABU      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-2L-AAQI      TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I5 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-3A-A9I7      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-3A-A9IH      TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-6879 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-F2-A44H      TCGA-F2-A7TX      TCGA-F2-A8YN 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A545      TCGA-FB-A5VM 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-7919 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-7922      TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-8003      TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-8519      TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A49H      TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7646      TCGA-IB-7647 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7886      TCGA-IB-7887 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7891      TCGA-IB-7893 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7897      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-US-A776      TCGA-US-A779 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-US-A77E      TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XD-AAUL      TCGA-YB-A89D      TCGA-YH-A8SY 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
D56V14, binary
                 cls
clus                0   1
  NAA20 MUTATED     0   2
  NAA20 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      0    2
  NAA20 WILD-TYPE    3  102
                        clus
vv                       NAA20 MUTATED NAA20 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(57) Variable = TRPC4 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  TRPC4 MUTATED    3  3
  TRPC4 WILD-TYPE 59 69
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             128 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              3              69 
$`TRPC4 MUTATED`
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-8126 
       17.00         5.88        13.84         0.23        19.82         2.47 

$`TRPC4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 
       71.74        10.98         7.66        19.27         3.12        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         1.08        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 
       15.81        19.66        21.30         3.85        15.98        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  TRPC4 MUTATED TRPC4 WILD-TYPE 
           0.23            0.13 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
          19.82           75.12 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
          9.860          13.745 
[1] "0.2 - 19.8 (9.9)"  "0.1 - 75.1 (13.7)"
[1] "hr=" "1.6"
D57V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TRPC4 MUTATED          0        1         1         3         1        0
  TRPC4 WILD-TYPE        4        5        19        96         3        3
D57V3, multiclass
           clus
vv          TRPC4 MUTATED TRPC4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             1              19
  STAGE IIB             3              96
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TRPC4 MUTATED     0   1     5
  TRPC4 WILD-TYPE   5  12   113
D57V4, multiclass
       clus
vv      TRPC4 MUTATED TRPC4 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                 cls
clus                0   1
  TRPC4 MUTATED     2   4
  TRPC4 WILD-TYPE  30 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      2    4
  TRPC4 WILD-TYPE   30  100
   clus
vv  TRPC4 MUTATED TRPC4 WILD-TYPE
  0             2              30
  1             4             100
[1] 2 2
[1] FALSE
D57V6, binary
                 cls
clus               0  1
  TRPC4 MUTATED    3  0
  TRPC4 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      3    0
  TRPC4 WILD-TYPE   59    3
   clus
vv  TRPC4 MUTATED TRPC4 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus               0  1
  TRPC4 MUTATED    4  2
  TRPC4 WILD-TYPE 58 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      4    2
  TRPC4 WILD-TYPE   58   72
        clus
vv       TRPC4 MUTATED TRPC4 WILD-TYPE
  FEMALE             4              58
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TRPC4 MUTATED                                     5
  TRPC4 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TRPC4 MUTATED                                       1
  TRPC4 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TRPC4 MUTATED                                                  0
  TRPC4 WILD-TYPE                                                2
D57V8, multiclass
                                                  clus
vv                                                 TRPC4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TRPC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, continuous
D57V10, continuous
                 vv
clus              R0 R1 R2 RX
  TRPC4 MUTATED    3  2  0  0
  TRPC4 WILD-TYPE 74 46  1  3
D57V11, multiclass
    clus
vv   TRPC4 MUTATED TRPC4 WILD-TYPE
  R0             3              74
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRPC4 MUTATED       0                         0     6
  TRPC4 WILD-TYPE     2                         5   119
D57V13, multiclass
                           clus
vv                          TRPC4 MUTATED TRPC4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                 cls
clus               0  1
  TRPC4 MUTATED    0  6
  TRPC4 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      0    6
  TRPC4 WILD-TYPE    3   98
                        clus
vv                       TRPC4 MUTATED TRPC4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(58) Variable = CHRNA9 MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2               0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 61 69
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              130 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               3               69 
$`CHRNA9 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQL TCGA-3A-A9IB TCGA-IB-A6UF 
        4.70         9.60         7.36        21.90 

$`CHRNA9 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 
        9.11        21.44        22.49         3.39        12.95        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       23.61        20.84        24.26        28.73        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        12.39        75.12        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
            4.70             0.13 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
           21.90            75.12 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
           8.480           13.825 
[1] "4.7 - 21.9 (8.5)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.2"
D58V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CHRNA9 MUTATED          0        0         0         4         0        0
  CHRNA9 WILD-TYPE        4        6        20        95         4        3
D58V3, multiclass
           clus
vv          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CHRNA9 MUTATED     0   0     4
  CHRNA9 WILD-TYPE   5  13   114
D58V4, multiclass
       clus
vv      CHRNA9 MUTATED CHRNA9 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                  cls
clus                 0   1
  CHRNA9 MUTATED     0   4
  CHRNA9 WILD-TYPE  32 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    4
  CHRNA9 WILD-TYPE   32  100
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              0               32
  1              4              100
[1] 2 2
[1] FALSE
D58V6, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  0
  CHRNA9 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    0
  CHRNA9 WILD-TYPE   61    3
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D58V7, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 61 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    3
  CHRNA9 WILD-TYPE   61   71
        clus
vv       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  FEMALE              1               61
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHRNA9 MUTATED                                     4
  CHRNA9 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHRNA9 MUTATED                                       0
  CHRNA9 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHRNA9 MUTATED                                                  0
  CHRNA9 WILD-TYPE                                                2
D58V8, multiclass
                                                  clus
vv                                                 CHRNA9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CHRNA9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, continuous
D58V10, continuous
[1] "Remove cluster labels:" "CHRNA9 MUTATED"        
clus
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-YY-A8LH 
"CHRNA9 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CHRNA9 MUTATED    1  2  0  1
  CHRNA9 WILD-TYPE 76 46  1  2
D58V11, multiclass
    clus
vv   CHRNA9 MUTATED CHRNA9 WILD-TYPE
  R0              1               76
  R1              2               46
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHRNA9 MUTATED       0                         0     4
  CHRNA9 WILD-TYPE     2                         5   121
D58V13, multiclass
                           clus
vv                          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                  cls
clus                 0   1
  CHRNA9 MUTATED     0   2
  CHRNA9 WILD-TYPE   3 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    2
  CHRNA9 WILD-TYPE    3  102
                        clus
vv                       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(59) Variable = SP140 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  SP140 MUTATED    0  4
  SP140 WILD-TYPE 62 68
  SP140 MUTATED SP140 WILD-TYPE 
              4             130 
  SP140 MUTATED SP140 WILD-TYPE 
              4              68 
$`SP140 MUTATED`
TCGA-2J-AAB6 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SS 
        9.63        20.19        19.82        15.12 

$`SP140 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  SP140 MUTATED SP140 WILD-TYPE 
           9.63            0.13 
  SP140 MUTATED SP140 WILD-TYPE 
          20.19           75.12 
  SP140 MUTATED SP140 WILD-TYPE 
          17.47           13.50 
[1] "9.6 - 20.2 (17.5)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.9"
D59V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SP140 MUTATED          0        0         1         4         0        0
  SP140 WILD-TYPE        4        6        19        95         4        3
D59V3, multiclass
           clus
vv          SP140 MUTATED SP140 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SP140 MUTATED     0   0     5
  SP140 WILD-TYPE   5  13   113
D59V4, multiclass
       clus
vv      SP140 MUTATED SP140 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                 cls
clus                0   1
  SP140 MUTATED     1   4
  SP140 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      1    4
  SP140 WILD-TYPE   31  100
   clus
vv  SP140 MUTATED SP140 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D59V6, binary
                 cls
clus               0  1
  SP140 MUTATED    3  0
  SP140 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      3    0
  SP140 WILD-TYPE   59    3
   clus
vv  SP140 MUTATED SP140 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus               0  1
  SP140 MUTATED    2  3
  SP140 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      2    3
  SP140 WILD-TYPE   60   71
        clus
vv       SP140 MUTATED SP140 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SP140 MUTATED                                     5
  SP140 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SP140 MUTATED                                       0
  SP140 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SP140 MUTATED                                                  0
  SP140 WILD-TYPE                                                2
D59V8, multiclass
                                                  clus
vv                                                 SP140 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SP140 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, continuous
D59V10, continuous
                 vv
clus              R0 R1 R2 RX
  SP140 MUTATED    5  0  0  0
  SP140 WILD-TYPE 72 48  1  3
D59V11, multiclass
    clus
vv   SP140 MUTATED SP140 WILD-TYPE
  R0             5              72
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP140 MUTATED       0                         0     5
  SP140 WILD-TYPE     2                         5   120
D59V13, multiclass
                           clus
vv                          SP140 MUTATED SP140 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                 cls
clus                0   1
  SP140 MUTATED     0   4
  SP140 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      0    4
  SP140 WILD-TYPE    3  100
                        clus
vv                       SP140 MUTATED SP140 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(60) Variable = KCNA7 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2              0  1
  KCNA7 MUTATED    2  3
  KCNA7 WILD-TYPE 60 69
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             129 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              3              69 
$`KCNA7 MUTATED`
TCGA-FB-A4P6 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-US-A77G 
       11.93        19.82        23.80         4.04         0.39 

$`KCNA7 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7887 
       49.38         4.77        21.90        15.35        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       14.14        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  KCNA7 MUTATED KCNA7 WILD-TYPE 
           0.39            0.13 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
          23.80           75.12 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
          11.93           13.81 
[1] "0.4 - 23.8 (11.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.4"
D60V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KCNA7 MUTATED          0        0         0         5         0        0
  KCNA7 WILD-TYPE        4        6        20        94         4        3
D60V3, multiclass
           clus
vv          KCNA7 MUTATED KCNA7 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KCNA7 MUTATED     0   0     5
  KCNA7 WILD-TYPE   5  13   113
D60V4, multiclass
       clus
vv      KCNA7 MUTATED KCNA7 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                 cls
clus               0  1
  KCNA7 MUTATED    0  5
  KCNA7 WILD-TYPE 32 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      0    5
  KCNA7 WILD-TYPE   32   99
   clus
vv  KCNA7 MUTATED KCNA7 WILD-TYPE
  0             0              32
  1             5              99
[1] 2 2
[1] FALSE
D60V6, binary
                 cls
clus               0  1
  KCNA7 MUTATED    3  0
  KCNA7 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      3    0
  KCNA7 WILD-TYPE   59    3
   clus
vv  KCNA7 MUTATED KCNA7 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus               0  1
  KCNA7 MUTATED    2  3
  KCNA7 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      2    3
  KCNA7 WILD-TYPE   60   71
        clus
vv       KCNA7 MUTATED KCNA7 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNA7 MUTATED                                     5
  KCNA7 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNA7 MUTATED                                       0
  KCNA7 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNA7 MUTATED                                                  0
  KCNA7 WILD-TYPE                                                2
D60V8, multiclass
                                                  clus
vv                                                 KCNA7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KCNA7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, continuous
D60V10, continuous
                 vv
clus              R0 R1 R2 RX
  KCNA7 MUTATED    2  2  0  0
  KCNA7 WILD-TYPE 75 46  1  3
D60V11, multiclass
    clus
vv   KCNA7 MUTATED KCNA7 WILD-TYPE
  R0             2              75
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNA7 MUTATED       1                         0     4
  KCNA7 WILD-TYPE     1                         5   121
D60V13, multiclass
                           clus
vv                          KCNA7 MUTATED KCNA7 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                 cls
clus               0  1
  KCNA7 MUTATED    0  5
  KCNA7 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      0    5
  KCNA7 WILD-TYPE    3   99
                        clus
vv                       KCNA7 MUTATED KCNA7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(61) Variable = AQP7 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2             0  1
  AQP7 MUTATED    4  3
  AQP7 WILD-TYPE 58 69
  AQP7 MUTATED AQP7 WILD-TYPE 
             7            127 
  AQP7 MUTATED AQP7 WILD-TYPE 
             3             69 
$`AQP7 MUTATED`
TCGA-3A-A9IH TCGA-3A-A9IZ TCGA-FB-A545 TCGA-H6-8124 TCGA-IB-7651 TCGA-XD-AAUL 
       28.73        10.13        24.07        12.89        19.82        13.32 
TCGA-YB-A89D 
       11.51 

$`AQP7 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       15.06        34.09        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HZ-7919 
       15.55         4.04         5.03         1.02        13.84        19.50 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.13        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YH-A8SY TCGA-YY-A8LH 
        0.39        13.81        12.99        12.03        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  AQP7 MUTATED AQP7 WILD-TYPE 
         10.13           0.13 
  AQP7 MUTATED AQP7 WILD-TYPE 
         28.73          75.12 
  AQP7 MUTATED AQP7 WILD-TYPE 
         13.32          13.81 
[1] "10.1 - 28.7 (13.3)" "0.1 - 75.1 (13.8)" 
[1] "hr=" "1.5"
D61V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AQP7 MUTATED          1        0         1         5         0        0
  AQP7 WILD-TYPE        3        6        19        94         4        3
D61V3, multiclass
           clus
vv          AQP7 MUTATED AQP7 WILD-TYPE
  STAGE IA             1              3
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  AQP7 MUTATED     1   0     6
  AQP7 WILD-TYPE   4  13   112
D61V4, multiclass
       clus
vv      AQP7 MUTATED AQP7 WILD-TYPE
  T1               1              4
  T2               0             13
  T3+T4            6            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                cls
clus              0  1
  AQP7 MUTATED    2  5
  AQP7 WILD-TYPE 30 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      2    5
  AQP7 WILD-TYPE   30   99
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            2             30
  1            5             99
[1] 2 2
[1] FALSE
D61V6, binary
                cls
clus              0  1
  AQP7 MUTATED    3  0
  AQP7 WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      3    0
  AQP7 WILD-TYPE   59    3
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus              0  1
  AQP7 MUTATED    4  3
  AQP7 WILD-TYPE 58 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      4    3
  AQP7 WILD-TYPE   58   71
        clus
vv       AQP7 MUTATED AQP7 WILD-TYPE
  FEMALE            4             58
  MALE              3             71
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AQP7 MUTATED                                     7
  AQP7 WILD-TYPE                                 115
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AQP7 MUTATED                                       0
  AQP7 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AQP7 MUTATED                                                  0
  AQP7 WILD-TYPE                                                2
D61V8, multiclass
                                                  clus
vv                                                 AQP7 MUTATED AQP7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7            115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, continuous
D61V10, continuous
                vv
clus             R0 R1 R2 RX
  AQP7 MUTATED    5  1  0  0
  AQP7 WILD-TYPE 72 47  1  3
D61V11, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  R0            5             72
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AQP7 MUTATED       0                         0     7
  AQP7 WILD-TYPE     2                         5   118
D61V13, multiclass
                           clus
vv                          AQP7 MUTATED AQP7 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                cls
clus              0  1
  AQP7 MUTATED    1  6
  AQP7 WILD-TYPE  2 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      1    6
  AQP7 WILD-TYPE    2   98
                        clus
vv                       AQP7 MUTATED AQP7 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            6             98
[1] 2 2
[1] FALSE

Clustering(62) Variable = SKA3 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2             0  1
  SKA3 MUTATED    4  2
  SKA3 WILD-TYPE 58 70
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            128 
  SKA3 MUTATED SKA3 WILD-TYPE 
             2             70 
$`SKA3 MUTATED`
TCGA-2J-AABF TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-A6UF TCGA-Q3-AA2A TCGA-YH-A8SY 
       22.72        19.82        23.80        21.90         3.12        12.76 

$`SKA3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.22        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 
       49.38         4.77        21.90        15.35        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
        8.78        15.45        13.68        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  SKA3 MUTATED SKA3 WILD-TYPE 
          3.12           0.13 
  SKA3 MUTATED SKA3 WILD-TYPE 
         23.80          75.12 
  SKA3 MUTATED SKA3 WILD-TYPE 
         20.86          13.50 
[1] "3.1 - 23.8 (20.9)" "0.1 - 75.1 (13.5)"
[1] "hr=" "2.2"
D62V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SKA3 MUTATED          0        1         0         4         1        0
  SKA3 WILD-TYPE        4        5        20        95         3        3
D62V3, multiclass
           clus
vv          SKA3 MUTATED SKA3 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             1              5
  STAGE IIA            0             20
  STAGE IIB            4             95
  STAGE III            1              3
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  SKA3 MUTATED     0   0     6
  SKA3 WILD-TYPE   5  13   112
D62V4, multiclass
       clus
vv      SKA3 MUTATED SKA3 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            6            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                cls
clus              0  1
  SKA3 MUTATED    0  6
  SKA3 WILD-TYPE 32 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      0    6
  SKA3 WILD-TYPE   32   98
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            0             32
  1            6             98
[1] 2 2
[1] FALSE
D62V6, binary
                cls
clus              0  1
  SKA3 MUTATED    4  0
  SKA3 WILD-TYPE 58  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    0
  SKA3 WILD-TYPE   58    3
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            4             58
  1            0              3
[1] 2 2
[1] FALSE
D62V7, binary
                cls
clus              0  1
  SKA3 MUTATED    4  2
  SKA3 WILD-TYPE 58 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    2
  SKA3 WILD-TYPE   58   72
        clus
vv       SKA3 MUTATED SKA3 WILD-TYPE
  FEMALE            4             58
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SKA3 MUTATED                                     5
  SKA3 WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SKA3 MUTATED                                       0
  SKA3 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SKA3 MUTATED                                                  0
  SKA3 WILD-TYPE                                                2
D62V8, multiclass
                                                  clus
vv                                                 SKA3 MUTATED SKA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, continuous
D62V10, continuous
                vv
clus             R0 R1 R2 RX
  SKA3 MUTATED    1  3  0  1
  SKA3 WILD-TYPE 76 45  1  2
D62V11, multiclass
    clus
vv   SKA3 MUTATED SKA3 WILD-TYPE
  R0            1             76
  R1            3             45
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SKA3 MUTATED       1                         0     5
  SKA3 WILD-TYPE     1                         5   120
D62V13, multiclass
                           clus
vv                          SKA3 MUTATED SKA3 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                cls
clus              0  1
  SKA3 MUTATED    0  5
  SKA3 WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      0    5
  SKA3 WILD-TYPE    3   99
                        clus
vv                       SKA3 MUTATED SKA3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             99
[1] 2 2
[1] FALSE

Clustering(63) Variable = DAAM1 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  DAAM1 MUTATED    1  5
  DAAM1 WILD-TYPE 61 67
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             128 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              5              67 
$`DAAM1 MUTATED`
TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7887 
       17.03         3.95        17.92        19.82        23.80         3.62 

$`DAAM1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 
       21.90        15.35        41.33         4.04        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  DAAM1 MUTATED DAAM1 WILD-TYPE 
           3.62            0.13 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
          23.80           75.12 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
         17.475          13.500 
[1] "3.6 - 23.8 (17.5)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.6"
D63V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DAAM1 MUTATED          0        0         0         5         0        1
  DAAM1 WILD-TYPE        4        6        20        94         4        2
D63V3, multiclass
           clus
vv          DAAM1 MUTATED DAAM1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  DAAM1 MUTATED     0   0     6
  DAAM1 WILD-TYPE   5  13   112
D63V4, multiclass
       clus
vv      DAAM1 MUTATED DAAM1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             6             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                 cls
clus               0  1
  DAAM1 MUTATED    1  5
  DAAM1 WILD-TYPE 31 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      1    5
  DAAM1 WILD-TYPE   31   99
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             1              31
  1             5              99
[1] 2 2
[1] FALSE
D63V6, binary
                 cls
clus               0  1
  DAAM1 MUTATED    3  1
  DAAM1 WILD-TYPE 59  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      3    1
  DAAM1 WILD-TYPE   59    2
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             3              59
  1             1               2
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus               0  1
  DAAM1 MUTATED    4  2
  DAAM1 WILD-TYPE 58 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      4    2
  DAAM1 WILD-TYPE   58   72
        clus
vv       DAAM1 MUTATED DAAM1 WILD-TYPE
  FEMALE             4              58
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DAAM1 MUTATED                                     6
  DAAM1 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DAAM1 MUTATED                                       0
  DAAM1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DAAM1 MUTATED                                                  0
  DAAM1 WILD-TYPE                                                2
D63V8, multiclass
                                                  clus
vv                                                 DAAM1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DAAM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, continuous
[1] "Remove cluster labels:" "DAAM1 MUTATED"         
clus
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
D63V10, continuous
[1] "Remove cluster labels:" "DAAM1 MUTATED"         
clus
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DAAM1 MUTATED    1  4  0  1
  DAAM1 WILD-TYPE 76 44  1  2
D63V11, multiclass
    clus
vv   DAAM1 MUTATED DAAM1 WILD-TYPE
  R0             1              76
  R1             4              44
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAAM1 MUTATED       1                         1     4
  DAAM1 WILD-TYPE     1                         4   121
D63V13, multiclass
                           clus
vv                          DAAM1 MUTATED DAAM1 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                 cls
clus               0  1
  DAAM1 MUTATED    0  6
  DAAM1 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      0    6
  DAAM1 WILD-TYPE    3   98
                        clus
vv                       DAAM1 MUTATED DAAM1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(64) Variable = MSH2 MUTATION ANALYSIS
D64V1, survival
                sevent
clus2             0  1
  MSH2 MUTATED    1  3
  MSH2 WILD-TYPE 61 69
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            130 
  MSH2 MUTATED MSH2 WILD-TYPE 
             3             69 
$`MSH2 MUTATED`
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-IB-7651 TCGA-IB-7887 
       23.21        12.03        19.82         3.62 

$`MSH2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       17.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  MSH2 MUTATED MSH2 WILD-TYPE 
          3.62           0.13 
  MSH2 MUTATED MSH2 WILD-TYPE 
         23.21          75.12 
  MSH2 MUTATED MSH2 WILD-TYPE 
        15.925         13.745 
[1] "3.6 - 23.2 (15.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D64V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MSH2 MUTATED          0        0         0         3         1        0
  MSH2 WILD-TYPE        4        6        20        96         3        3
D64V3, multiclass
           clus
vv          MSH2 MUTATED MSH2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            1              3
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  MSH2 MUTATED     0   0     4
  MSH2 WILD-TYPE   5  13   114
D64V4, multiclass
       clus
vv      MSH2 MUTATED MSH2 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                cls
clus               0   1
  MSH2 MUTATED     1   3
  MSH2 WILD-TYPE  31 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      1    3
  MSH2 WILD-TYPE   31  101
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0            1             31
  1            3            101
[1] 2 2
[1] FALSE
D64V6, binary
                cls
clus              0  1
  MSH2 MUTATED    2  0
  MSH2 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      2    0
  MSH2 WILD-TYPE   60    3
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D64V7, binary
                cls
clus              0  1
  MSH2 MUTATED    2  2
  MSH2 WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      2    2
  MSH2 WILD-TYPE   60   72
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MSH2 MUTATED                                     4
  MSH2 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MSH2 MUTATED                                       0
  MSH2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MSH2 MUTATED                                                  0
  MSH2 WILD-TYPE                                                2
D64V8, multiclass
                                                  clus
vv                                                 MSH2 MUTATED MSH2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, continuous
[1] "Remove cluster labels:" "MSH2 MUTATED"          
clus
  MSH2 MUTATED MSH2 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
D64V10, continuous
[1] "Remove cluster labels:" "MSH2 MUTATED"          
clus
  MSH2 MUTATED MSH2 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MSH2 MUTATED    3  1  0  0
  MSH2 WILD-TYPE 74 47  1  3
D64V11, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0            3             74
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MSH2 MUTATED       0                         0     4
  MSH2 WILD-TYPE     2                         5   121
D64V13, multiclass
                           clus
vv                          MSH2 MUTATED MSH2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                cls
clus               0   1
  MSH2 MUTATED     0   4
  MSH2 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      0    4
  MSH2 WILD-TYPE    3  100
                        clus
vv                       MSH2 MUTATED MSH2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(65) Variable = NUP210L MUTATION ANALYSIS
D65V1, survival
                   sevent
clus2                0  1
  NUP210L MUTATED    3  2
  NUP210L WILD-TYPE 59 70
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               129 
  NUP210L MUTATED NUP210L WILD-TYPE 
                2                70 
$`NUP210L MUTATED`
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5ST TCGA-US-A776 
       15.35        19.82        41.33        20.88        27.75 

$`NUP210L WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7886 
       12.95        49.38         4.77        21.90        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  NUP210L MUTATED NUP210L WILD-TYPE 
            15.35              0.13 
  NUP210L MUTATED NUP210L WILD-TYPE 
            41.33             75.12 
  NUP210L MUTATED NUP210L WILD-TYPE 
            20.88             12.99 
[1] "15.3 - 41.3 (20.9)" "0.1 - 75.1 (13.0)" 
[1] "hr=" "2.5"
D65V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NUP210L MUTATED          0        0         1         4         0        0
  NUP210L WILD-TYPE        4        6        19        95         4        3
D65V3, multiclass
           clus
vv          NUP210L MUTATED NUP210L WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               1                19
  STAGE IIB               4                95
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  NUP210L MUTATED     0   0     5
  NUP210L WILD-TYPE   5  13   113
D65V4, multiclass
       clus
vv      NUP210L MUTATED NUP210L WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               5               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V5, binary
                   cls
clus                  0   1
  NUP210L MUTATED     1   4
  NUP210L WILD-TYPE  31 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      1    4
  NUP210L WILD-TYPE   31  100
   clus
vv  NUP210L MUTATED NUP210L WILD-TYPE
  0               1                31
  1               4               100
[1] 2 2
[1] FALSE
D65V6, binary
                   cls
clus                 0  1
  NUP210L MUTATED    4  0
  NUP210L WILD-TYPE 58  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      4    0
  NUP210L WILD-TYPE   58    3
   clus
vv  NUP210L MUTATED NUP210L WILD-TYPE
  0               4                58
  1               0                 3
[1] 2 2
[1] FALSE
D65V7, binary
                   cls
clus                 0  1
  NUP210L MUTATED    4  1
  NUP210L WILD-TYPE 58 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      4    1
  NUP210L WILD-TYPE   58   73
        clus
vv       NUP210L MUTATED NUP210L WILD-TYPE
  FEMALE               4                58
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NUP210L MUTATED                                     4
  NUP210L WILD-TYPE                                 118
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NUP210L MUTATED                                       0
  NUP210L WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NUP210L MUTATED                                                  1
  NUP210L WILD-TYPE                                                1
D65V8, multiclass
                                                  clus
vv                                                 NUP210L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 NUP210L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, continuous
D65V10, continuous
                   vv
clus                R0 R1 R2 RX
  NUP210L MUTATED    4  1  0  0
  NUP210L WILD-TYPE 73 47  1  3
D65V11, multiclass
    clus
vv   NUP210L MUTATED NUP210L WILD-TYPE
  R0               4                73
  R1               1                47
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP210L MUTATED       0                         0     4
  NUP210L WILD-TYPE     2                         5   121
D65V13, multiclass
                           clus
vv                          NUP210L MUTATED NUP210L WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                   cls
clus                  0   1
  NUP210L MUTATED     0   4
  NUP210L WILD-TYPE   3 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      0    4
  NUP210L WILD-TYPE    3  100
                        clus
vv                       NUP210L MUTATED NUP210L WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               100
[1] 2 2
[1] FALSE

Clustering(66) Variable = GPR98 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2              0  1
  GPR98 MUTATED    3  5
  GPR98 WILD-TYPE 59 67
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             126 
  GPR98 MUTATED GPR98 WILD-TYPE 
              5              67 
$`GPR98 MUTATED`
TCGA-3A-A9IU TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-IB-7649 TCGA-IB-7651 
       15.06        20.19        17.03        23.21        15.35        19.82 
TCGA-IB-7885 TCGA-LB-A8F3 
       41.33        12.46 

$`GPR98 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8002 TCGA-HZ-8003 
       12.89        13.84        19.50         0.13        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  GPR98 MUTATED GPR98 WILD-TYPE 
          12.46            0.13 
  GPR98 MUTATED GPR98 WILD-TYPE 
          41.33           75.12 
  GPR98 MUTATED GPR98 WILD-TYPE 
         18.425          12.970 
[1] "12.5 - 41.3 (18.4)" "0.1 - 75.1 (13.0)" 
[1] "hr=" "1.2"
D66V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPR98 MUTATED          0        0         1         6         1        0
  GPR98 WILD-TYPE        4        6        19        93         3        3
D66V3, multiclass
           clus
vv          GPR98 MUTATED GPR98 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             6              93
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  GPR98 MUTATED     0   0     8
  GPR98 WILD-TYPE   5  13   110
D66V4, multiclass
       clus
vv      GPR98 MUTATED GPR98 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             8             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                 cls
clus               0  1
  GPR98 MUTATED    2  6
  GPR98 WILD-TYPE 30 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      2    6
  GPR98 WILD-TYPE   30   98
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0             2              30
  1             6              98
[1] 2 2
[1] FALSE
D66V6, binary
                 cls
clus               0  1
  GPR98 MUTATED    3  0
  GPR98 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      3    0
  GPR98 WILD-TYPE   59    3
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus               0  1
  GPR98 MUTATED    4  4
  GPR98 WILD-TYPE 58 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      4    4
  GPR98 WILD-TYPE   58   70
        clus
vv       GPR98 MUTATED GPR98 WILD-TYPE
  FEMALE             4              58
  MALE               4              70
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR98 MUTATED                                     8
  GPR98 WILD-TYPE                                 114
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR98 MUTATED                                       0
  GPR98 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR98 MUTATED                                                  0
  GPR98 WILD-TYPE                                                2
D66V8, multiclass
                                                  clus
vv                                                 GPR98 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 GPR98 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          114
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, continuous
D66V10, continuous
                 vv
clus              R0 R1 R2 RX
  GPR98 MUTATED    6  1  0  1
  GPR98 WILD-TYPE 71 47  1  2
D66V11, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  R0             6              71
  R1             1              47
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR98 MUTATED       0                         2     5
  GPR98 WILD-TYPE     2                         3   120
D66V13, multiclass
                           clus
vv                          GPR98 MUTATED GPR98 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                 cls
clus               0  1
  GPR98 MUTATED    0  7
  GPR98 WILD-TYPE  3 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      0    7
  GPR98 WILD-TYPE    3   97
                        clus
vv                       GPR98 MUTATED GPR98 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7              97
[1] 2 2
[1] FALSE

Clustering(67) Variable = CD2AP MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2              0  1
  CD2AP MUTATED    0  3
  CD2AP WILD-TYPE 62 69
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             131 
  CD2AP MUTATED CD2AP WILD-TYPE 
              3              69 
$`CD2AP MUTATED`
TCGA-HZ-8005 TCGA-IB-7651 TCGA-IB-AAUO 
        3.95        19.82         7.86 

$`CD2AP WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CD2AP MUTATED CD2AP WILD-TYPE 
           3.95            0.13 
  CD2AP MUTATED CD2AP WILD-TYPE 
          19.82           75.12 
  CD2AP MUTATED CD2AP WILD-TYPE 
           7.86           13.81 
[1] "4.0 - 19.8 (7.9)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.1"
D67V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CD2AP MUTATED          0        0         0         3         0        0
  CD2AP WILD-TYPE        4        6        20        96         4        3
D67V3, multiclass
           clus
vv          CD2AP MUTATED CD2AP WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CD2AP MUTATED     0   0     3
  CD2AP WILD-TYPE   5  13   115
D67V4, multiclass
       clus
vv      CD2AP MUTATED CD2AP WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                 cls
clus                0   1
  CD2AP MUTATED     0   3
  CD2AP WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      0    3
  CD2AP WILD-TYPE   32  101
   clus
vv  CD2AP MUTATED CD2AP WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D67V6, binary
                 cls
clus               0  1
  CD2AP MUTATED    2  0
  CD2AP WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      2    0
  CD2AP WILD-TYPE   60    3
   clus
vv  CD2AP MUTATED CD2AP WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus               0  1
  CD2AP MUTATED    2  1
  CD2AP WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      2    1
  CD2AP WILD-TYPE   60   73
        clus
vv       CD2AP MUTATED CD2AP WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD2AP MUTATED                                     3
  CD2AP WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD2AP MUTATED                                       0
  CD2AP WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD2AP MUTATED                                                  0
  CD2AP WILD-TYPE                                                2
D67V8, multiclass
                                                  clus
vv                                                 CD2AP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CD2AP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, continuous
[1] "Remove cluster labels:" "CD2AP MUTATED"         
clus
  CD2AP MUTATED CD2AP WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
D67V10, continuous
[1] "Remove cluster labels:" "CD2AP MUTATED"         
clus
  CD2AP MUTATED CD2AP WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CD2AP MUTATED    1  2  0  0
  CD2AP WILD-TYPE 76 46  1  3
D67V11, multiclass
    clus
vv   CD2AP MUTATED CD2AP WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD2AP MUTATED       0                         0     3
  CD2AP WILD-TYPE     2                         5   122
D67V13, multiclass
                           clus
vv                          CD2AP MUTATED CD2AP WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                 cls
clus                0   1
  CD2AP MUTATED     0   3
  CD2AP WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      0    3
  CD2AP WILD-TYPE    3  101
                        clus
vv                       CD2AP MUTATED CD2AP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(68) Variable = RREB1 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    3  6
  RREB1 WILD-TYPE 59 66
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             125 
  RREB1 MUTATED RREB1 WILD-TYPE 
              6              66 
$`RREB1 MUTATED`
TCGA-2J-AABA TCGA-3A-A9I9 TCGA-FB-AAPS TCGA-HZ-7926 TCGA-IB-7651 TCGA-IB-7888 
       19.96        20.84         7.50        17.03        19.82        43.79 
TCGA-IB-A5SP TCGA-OE-A75W TCGA-YB-A89D 
       15.85         8.78        11.51 

$`RREB1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       53.00        23.61         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       24.07        14.76        12.43        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       19.50         0.13        20.19        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 
       15.35        23.80        41.33         4.04         3.62        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        12.76        66.28         0.69 

  RREB1 MUTATED RREB1 WILD-TYPE 
           7.50            0.13 
  RREB1 MUTATED RREB1 WILD-TYPE 
          43.79           75.12 
  RREB1 MUTATED RREB1 WILD-TYPE 
          17.03           13.32 
[1] "7.5 - 43.8 (17.0)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1"  
D68V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RREB1 MUTATED          0        0         4         5         0        0
  RREB1 WILD-TYPE        4        6        16        94         4        3
D68V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             4              16
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RREB1 MUTATED     0   1     8
  RREB1 WILD-TYPE   5  12   110
D68V4, multiclass
       clus
vv      RREB1 MUTATED RREB1 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             8             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                 cls
clus               0  1
  RREB1 MUTATED    4  5
  RREB1 WILD-TYPE 28 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      4    5
  RREB1 WILD-TYPE   28   99
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             4              28
  1             5              99
[1] 2 2
[1] FALSE
D68V6, binary
                 cls
clus               0  1
  RREB1 MUTATED    5  0
  RREB1 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      5    0
  RREB1 WILD-TYPE   57    3
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             5              57
  1             0               3
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    3  6
  RREB1 WILD-TYPE 59 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    6
  RREB1 WILD-TYPE   59   68
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             3              59
  MALE               6              68
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RREB1 MUTATED                                     9
  RREB1 WILD-TYPE                                 113
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RREB1 MUTATED                                       0
  RREB1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RREB1 MUTATED                                                  0
  RREB1 WILD-TYPE                                                2
D68V8, multiclass
                                                  clus
vv                                                 RREB1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RREB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          113
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, continuous
D68V10, continuous
                 vv
clus              R0 R1 R2 RX
  RREB1 MUTATED    6  2  0  1
  RREB1 WILD-TYPE 71 46  1  2
D68V11, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  R0             6              71
  R1             2              46
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RREB1 MUTATED       0                         2     7
  RREB1 WILD-TYPE     2                         3   118
D68V13, multiclass
                           clus
vv                          RREB1 MUTATED RREB1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 7             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                 cls
clus               0  1
  RREB1 MUTATED    0  7
  RREB1 WILD-TYPE  3 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      0    7
  RREB1 WILD-TYPE    3   97
                        clus
vv                       RREB1 MUTATED RREB1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7              97
[1] 2 2
[1] FALSE

Clustering(69) Variable = KIAA0586 MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  KIAA0586 MUTATED    1  5
  KIAA0586 WILD-TYPE 61 67
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                128 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 5                 67 
$`KIAA0586 MUTATED`
TCGA-HZ-8002 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7887 TCGA-IB-8127 TCGA-IB-AAUN 
       12.03        15.35        19.82         3.62        17.16         4.73 

$`KIAA0586 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       49.38         4.77        21.90        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO 
       21.90         1.35         8.22        15.88         0.26         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
              3.62               0.13 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
             19.82              75.12 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
            13.690             13.745 
[1] "3.6 - 19.8 (13.7)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.2"
D69V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KIAA0586 MUTATED          0        1         0         5         0        0
  KIAA0586 WILD-TYPE        4        5        20        94         4        3
D69V3, multiclass
           clus
vv          KIAA0586 MUTATED KIAA0586 WILD-TYPE
  STAGE IA                 0                  4
  STAGE IB                 1                  5
  STAGE IIA                0                 20
  STAGE IIB                5                 94
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  KIAA0586 MUTATED     0   1     5
  KIAA0586 WILD-TYPE   5  12   113
D69V4, multiclass
       clus
vv      KIAA0586 MUTATED KIAA0586 WILD-TYPE
  T1                   0                  5
  T2                   1                 12
  T3+T4                5                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V5, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    1  5
  KIAA0586 WILD-TYPE 31 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      1    5
  KIAA0586 WILD-TYPE   31   99
   clus
vv  KIAA0586 MUTATED KIAA0586 WILD-TYPE
  0                1                 31
  1                5                 99
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    5  0
  KIAA0586 WILD-TYPE 57  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      5    0
  KIAA0586 WILD-TYPE   57    3
   clus
vv  KIAA0586 MUTATED KIAA0586 WILD-TYPE
  0                5                 57
  1                0                  3
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    4  2
  KIAA0586 WILD-TYPE 58 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      4    2
  KIAA0586 WILD-TYPE   58   72
        clus
vv       KIAA0586 MUTATED KIAA0586 WILD-TYPE
  FEMALE                4                 58
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0586 MUTATED                                     6
  KIAA0586 WILD-TYPE                                 116
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0586 MUTATED                                       0
  KIAA0586 WILD-TYPE                                    11
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0586 MUTATED                                                  0
  KIAA0586 WILD-TYPE                                                2
D69V8, multiclass
                                                  clus
vv                                                 KIAA0586 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 KIAA0586 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, continuous
D69V10, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA0586 MUTATED    2  4  0  0
  KIAA0586 WILD-TYPE 75 44  1  3
D69V11, multiclass
    clus
vv   KIAA0586 MUTATED KIAA0586 WILD-TYPE
  R0                2                 75
  R1                4                 44
  R2                0                  1
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0586 MUTATED       0                         0     5
  KIAA0586 WILD-TYPE     2                         5   120
D69V13, multiclass
                           clus
vv                          KIAA0586 MUTATED KIAA0586 WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    0  5
  KIAA0586 WILD-TYPE  3 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      0    5
  KIAA0586 WILD-TYPE    3   99
                        clus
vv                       KIAA0586 MUTATED KIAA0586 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 99
[1] 2 2
[1] FALSE

Clustering(70) Variable = GNAS MUTATION ANALYSIS
D70V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    2  6
  GNAS WILD-TYPE 60 66
  GNAS MUTATED GNAS WILD-TYPE 
             8            126 
  GNAS MUTATED GNAS WILD-TYPE 
             6             66 
$`GNAS MUTATED`
TCGA-2J-AAB1 TCGA-F2-A44G TCGA-HZ-8317 TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUT 
        2.17         7.66        12.43        19.82        12.00         9.44 
TCGA-US-A776 TCGA-US-A77E 
       27.75        14.14 

$`GNAS WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         3.95         9.83        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       23.08        22.85        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  GNAS MUTATED GNAS WILD-TYPE 
          2.17           0.13 
  GNAS MUTATED GNAS WILD-TYPE 
         27.75          75.12 
  GNAS MUTATED GNAS WILD-TYPE 
        12.215         13.825 
[1] "2.2 - 27.8 (12.2)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.8"
D70V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GNAS MUTATED          0        0         1         7         0        0
  GNAS WILD-TYPE        4        6        19        92         4        3
D70V3, multiclass
           clus
vv          GNAS MUTATED GNAS WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            7             92
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  GNAS MUTATED     0   1     7
  GNAS WILD-TYPE   5  12   111
D70V4, multiclass
       clus
vv      GNAS MUTATED GNAS WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            7            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                cls
clus              0  1
  GNAS MUTATED    1  7
  GNAS WILD-TYPE 31 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      1    7
  GNAS WILD-TYPE   31   97
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            1             31
  1            7             97
[1] 2 2
[1] FALSE
D70V6, binary
                cls
clus              0  1
  GNAS MUTATED    5  0
  GNAS WILD-TYPE 57  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      5    0
  GNAS WILD-TYPE   57    3
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            5             57
  1            0              3
[1] 2 2
[1] FALSE
D70V7, binary
                cls
clus              0  1
  GNAS MUTATED    3  5
  GNAS WILD-TYPE 59 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      3    5
  GNAS WILD-TYPE   59   69
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            3             59
  MALE              5             69
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNAS MUTATED                                     4
  GNAS WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNAS MUTATED                                       2
  GNAS WILD-TYPE                                     9
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNAS MUTATED                                                  2
  GNAS WILD-TYPE                                                0
D70V8, multiclass
                                                  clus
vv                                                 GNAS MUTATED GNAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            2              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, continuous
D70V10, continuous
                vv
clus             R0 R1 R2 RX
  GNAS MUTATED    4  4  0  0
  GNAS WILD-TYPE 73 44  1  3
D70V11, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            4             73
  R1            4             44
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED       0                         0     8
  GNAS WILD-TYPE     2                         5   117
D70V13, multiclass
                           clus
vv                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                cls
clus              0  1
  GNAS MUTATED    0  6
  GNAS WILD-TYPE  3 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0    6
  GNAS WILD-TYPE    3   98
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6             98
[1] 2 2
[1] FALSE

Clustering(71) Variable = FAR1 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2             0  1
  FAR1 MUTATED    2  2
  FAR1 WILD-TYPE 60 70
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            130 
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             70 
$`FAR1 MUTATED`
TCGA-3A-A9J0 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       12.39        20.19        19.82        41.33 

$`FAR1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        34.09        10.13        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  FAR1 MUTATED FAR1 WILD-TYPE 
         12.39           0.13 
  FAR1 MUTATED FAR1 WILD-TYPE 
         41.33          75.12 
  FAR1 MUTATED FAR1 WILD-TYPE 
        20.005         13.500 
[1] "12.4 - 41.3 (20.0)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.7"
D71V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FAR1 MUTATED          0        0         0         4         0        0
  FAR1 WILD-TYPE        4        6        20        95         4        3
D71V3, multiclass
           clus
vv          FAR1 MUTATED FAR1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            4             95
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  FAR1 MUTATED     0   0     4
  FAR1 WILD-TYPE   5  13   114
D71V4, multiclass
       clus
vv      FAR1 MUTATED FAR1 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                cls
clus               0   1
  FAR1 MUTATED     0   4
  FAR1 WILD-TYPE  32 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      0    4
  FAR1 WILD-TYPE   32  100
   clus
vv  FAR1 MUTATED FAR1 WILD-TYPE
  0            0             32
  1            4            100
[1] 2 2
[1] FALSE
D71V6, binary
                cls
clus              0  1
  FAR1 MUTATED    2  0
  FAR1 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      2    0
  FAR1 WILD-TYPE   60    3
   clus
vv  FAR1 MUTATED FAR1 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D71V7, binary
                cls
clus              0  1
  FAR1 MUTATED    2  2
  FAR1 WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      2    2
  FAR1 WILD-TYPE   60   72
        clus
vv       FAR1 MUTATED FAR1 WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAR1 MUTATED                                     4
  FAR1 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAR1 MUTATED                                       0
  FAR1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAR1 MUTATED                                                  0
  FAR1 WILD-TYPE                                                2
D71V8, multiclass
                                                  clus
vv                                                 FAR1 MUTATED FAR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, continuous
[1] "Remove cluster labels:" "FAR1 MUTATED"          
clus
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7891 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
D71V10, continuous
[1] "Remove cluster labels:" "FAR1 MUTATED"          
clus
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7891 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-YY-A8LH 
"FAR1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  FAR1 MUTATED    4  0  0  0
  FAR1 WILD-TYPE 73 48  1  3
D71V11, multiclass
    clus
vv   FAR1 MUTATED FAR1 WILD-TYPE
  R0            4             73
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAR1 MUTATED       0                         0     4
  FAR1 WILD-TYPE     2                         5   121
D71V13, multiclass
                           clus
vv                          FAR1 MUTATED FAR1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                cls
clus               0   1
  FAR1 MUTATED     0   4
  FAR1 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      0    4
  FAR1 WILD-TYPE    3  100
                        clus
vv                       FAR1 MUTATED FAR1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(72) Variable = OR2T4 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2              0  1
  OR2T4 MUTATED    3  1
  OR2T4 WILD-TYPE 59 71
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              4             130 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              1              71 
$`OR2T4 MUTATED`
TCGA-HZ-8003 TCGA-HZ-A49H TCGA-IB-7651 TCGA-US-A776 
        0.69        16.14        19.82        27.75 

$`OR2T4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        21.70        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 
        9.40        21.24        17.26        23.08        22.85        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  OR2T4 MUTATED OR2T4 WILD-TYPE 
           0.69            0.13 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
          27.75           75.12 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
          17.98           13.50 
[1] "0.7 - 27.8 (18.0)" "0.1 - 75.1 (13.5)"
[1] "hr=" "2.7"
D72V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR2T4 MUTATED          0        0         1         3         0        0
  OR2T4 WILD-TYPE        4        6        19        96         4        3
D72V3, multiclass
           clus
vv          OR2T4 MUTATED OR2T4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  OR2T4 MUTATED     0   0     4
  OR2T4 WILD-TYPE   5  13   114
D72V4, multiclass
       clus
vv      OR2T4 MUTATED OR2T4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                 cls
clus                0   1
  OR2T4 MUTATED     1   3
  OR2T4 WILD-TYPE  31 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      1    3
  OR2T4 WILD-TYPE   31  101
   clus
vv  OR2T4 MUTATED OR2T4 WILD-TYPE
  0             1              31
  1             3             101
[1] 2 2
[1] FALSE
D72V6, binary
                 cls
clus               0  1
  OR2T4 MUTATED    1  0
  OR2T4 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      1    0
  OR2T4 WILD-TYPE   61    3
   clus
vv  OR2T4 MUTATED OR2T4 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus               0  1
  OR2T4 MUTATED    3  1
  OR2T4 WILD-TYPE 59 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      3    1
  OR2T4 WILD-TYPE   59   73
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  FEMALE             3              59
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR2T4 MUTATED                                     3
  OR2T4 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR2T4 MUTATED                                       0
  OR2T4 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR2T4 MUTATED                                                  1
  OR2T4 WILD-TYPE                                                1
D72V8, multiclass
                                                  clus
vv                                                 OR2T4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 OR2T4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, continuous
[1] "Remove cluster labels:" "OR2T4 MUTATED"         
clus
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
D72V10, continuous
[1] "Remove cluster labels:" "OR2T4 MUTATED"         
clus
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR2T4 MUTATED    4  0  0  0
  OR2T4 WILD-TYPE 73 48  1  3
D72V11, multiclass
    clus
vv   OR2T4 MUTATED OR2T4 WILD-TYPE
  R0             4              73
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2T4 MUTATED       0                         0     4
  OR2T4 WILD-TYPE     2                         5   121
D72V13, multiclass
                           clus
vv                          OR2T4 MUTATED OR2T4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                 cls
clus                0   1
  OR2T4 MUTATED     0   4
  OR2T4 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      0    4
  OR2T4 WILD-TYPE    3  100
                        clus
vv                       OR2T4 MUTATED OR2T4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(73) Variable = GPR50 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2              0  1
  GPR50 MUTATED    2  3
  GPR50 WILD-TYPE 60 69
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             129 
  GPR50 MUTATED GPR50 WILD-TYPE 
              3              69 
$`GPR50 MUTATED`
TCGA-3A-A9I9 TCGA-HZ-8001 TCGA-HZ-8005 TCGA-HZ-A49H TCGA-IB-7893 
       20.84        23.21         3.95        16.14         3.85 

$`GPR50 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        53.00        23.61         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       21.70        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.81        19.66        21.30        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  GPR50 MUTATED GPR50 WILD-TYPE 
           3.85            0.13 
  GPR50 MUTATED GPR50 WILD-TYPE 
          23.21           75.12 
  GPR50 MUTATED GPR50 WILD-TYPE 
          16.14           13.68 
[1] "3.9 - 23.2 (16.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D73V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPR50 MUTATED          0        0         2         2         1        0
  GPR50 WILD-TYPE        4        6        18        97         3        3
D73V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             2              97
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  GPR50 MUTATED     0   0     5
  GPR50 WILD-TYPE   5  13   113
D73V4, multiclass
       clus
vv      GPR50 MUTATED GPR50 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE  29 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    2
  GPR50 WILD-TYPE   29  102
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3              29
  1             2             102
[1] 2 2
[1] FALSE
D73V6, binary
                 cls
clus               0  1
  GPR50 MUTATED    1  0
  GPR50 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    0
  GPR50 WILD-TYPE   61    3
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D73V7, binary
                 cls
clus               0  1
  GPR50 MUTATED    1  4
  GPR50 WILD-TYPE 61 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    4
  GPR50 WILD-TYPE   61   70
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             1              61
  MALE               4              70
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR50 MUTATED                                     5
  GPR50 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR50 MUTATED                                       0
  GPR50 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR50 MUTATED                                                  0
  GPR50 WILD-TYPE                                                2
D73V8, multiclass
                                                  clus
vv                                                 GPR50 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 GPR50 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
D73V10, continuous
                 vv
clus              R0 R1 R2 RX
  GPR50 MUTATED    4  1  0  0
  GPR50 WILD-TYPE 73 47  1  3
D73V11, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED       0                         0     5
  GPR50 WILD-TYPE     2                         5   120
D73V13, multiclass
                           clus
vv                          GPR50 MUTATED GPR50 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                 cls
clus               0  1
  GPR50 MUTATED    0  5
  GPR50 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    5
  GPR50 WILD-TYPE    3   99
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(74) Variable = TAX1BP1 MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                0  1
  TAX1BP1 MUTATED    1  4
  TAX1BP1 WILD-TYPE 61 68
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               129 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                4                68 
$`TAX1BP1 MUTATED`
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO 
       17.03        12.03        19.82        41.33        12.00 

$`TAX1BP1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            12.00              0.13 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            41.33             75.12 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            17.03             13.68 
[1] "12.0 - 41.3 (17.0)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "1.2"
D74V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TAX1BP1 MUTATED          0        0         0         5         0        0
  TAX1BP1 WILD-TYPE        4        6        20        94         4        3
D74V3, multiclass
           clus
vv          TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               5                94
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  TAX1BP1 MUTATED     0   0     5
  TAX1BP1 WILD-TYPE   5  13   113
D74V4, multiclass
       clus
vv      TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               5               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    0  5
  TAX1BP1 WILD-TYPE 32 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      0    5
  TAX1BP1 WILD-TYPE   32   99
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               0                32
  1               5                99
[1] 2 2
[1] FALSE
D74V6, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    3  0
  TAX1BP1 WILD-TYPE 59  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      3    0
  TAX1BP1 WILD-TYPE   59    3
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               3                59
  1               0                 3
[1] 2 2
[1] FALSE
D74V7, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    2  3
  TAX1BP1 WILD-TYPE 60 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      2    3
  TAX1BP1 WILD-TYPE   60   71
        clus
vv       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  FEMALE               2                60
  MALE                 3                71
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TAX1BP1 MUTATED                                     5
  TAX1BP1 WILD-TYPE                                 117
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TAX1BP1 MUTATED                                       0
  TAX1BP1 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TAX1BP1 MUTATED                                                  0
  TAX1BP1 WILD-TYPE                                                2
D74V8, multiclass
                                                  clus
vv                                                 TAX1BP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 TAX1BP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, continuous
[1] "Remove cluster labels:" "TAX1BP1 MUTATED"       
clus
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
D74V10, continuous
[1] "Remove cluster labels:" "TAX1BP1 MUTATED"       
clus
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                2                37 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7891 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-YY-A8LH 
"TAX1BP1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TAX1BP1 MUTATED    4  0  0  1
  TAX1BP1 WILD-TYPE 73 48  1  2
D74V11, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  R0               4                73
  R1               0                48
  R2               0                 1
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAX1BP1 MUTATED       0                         1     4
  TAX1BP1 WILD-TYPE     2                         4   121
D74V13, multiclass
                           clus
vv                          TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   4               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     0   4
  TAX1BP1 WILD-TYPE   3 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      0    4
  TAX1BP1 WILD-TYPE    3  100
                        clus
vv                       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               100
[1] 2 2
[1] FALSE

Clustering(75) Variable = CCDC33 MUTATION ANALYSIS
D75V1, survival
                  sevent
clus2               0  1
  CCDC33 MUTATED    0  3
  CCDC33 WILD-TYPE 62 69
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              131 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3               69 
$`CCDC33 MUTATED`
TCGA-F2-6879 TCGA-HZ-7926 TCGA-HZ-8005 
       10.98        17.03         3.95 

$`CCDC33 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CCDC33 MUTATED CCDC33 WILD-TYPE 
            3.95             0.13 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
           17.03            75.12 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
           10.98            13.81 
[1] "4.0 - 17.0 (11.0)" "0.1 - 75.1 (13.8)"
[1] "hr=" "3.1"
D75V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CCDC33 MUTATED          0        0         0         3         0        0
  CCDC33 WILD-TYPE        4        6        20        96         4        3
D75V3, multiclass
           clus
vv          CCDC33 MUTATED CCDC33 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CCDC33 MUTATED     0   0     3
  CCDC33 WILD-TYPE   5  13   115
D75V4, multiclass
       clus
vv      CCDC33 MUTATED CCDC33 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                  cls
clus                 0   1
  CCDC33 MUTATED     0   3
  CCDC33 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    3
  CCDC33 WILD-TYPE   32  101
   clus
vv  CCDC33 MUTATED CCDC33 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D75V6, binary
                  cls
clus                0  1
  CCDC33 MUTATED    1  0
  CCDC33 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      1    0
  CCDC33 WILD-TYPE   61    3
   clus
vv  CCDC33 MUTATED CCDC33 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D75V7, binary
                  cls
clus                0  1
  CCDC33 MUTATED    0  3
  CCDC33 WILD-TYPE 62 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    3
  CCDC33 WILD-TYPE   62   71
        clus
vv       CCDC33 MUTATED CCDC33 WILD-TYPE
  FEMALE              0               62
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC33 MUTATED                                     2
  CCDC33 WILD-TYPE                                 120
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC33 MUTATED                                       1
  CCDC33 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC33 MUTATED                                                  0
  CCDC33 WILD-TYPE                                                2
D75V8, multiclass
                                                  clus
vv                                                 CCDC33 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CCDC33 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, continuous
D75V10, continuous
                  vv
clus               R0 R1 R2 RX
  CCDC33 MUTATED    1  1  0  1
  CCDC33 WILD-TYPE 76 47  1  2
D75V11, multiclass
    clus
vv   CCDC33 MUTATED CCDC33 WILD-TYPE
  R0              1               76
  R1              1               47
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC33 MUTATED       0                         1     2
  CCDC33 WILD-TYPE     2                         4   123
D75V13, multiclass
                           clus
vv                          CCDC33 MUTATED CCDC33 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  2              123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                  cls
clus                 0   1
  CCDC33 MUTATED     0   2
  CCDC33 WILD-TYPE   3 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    2
  CCDC33 WILD-TYPE    3  102
                        clus
vv                       CCDC33 MUTATED CCDC33 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(76) Variable = JAK2 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2             0  1
  JAK2 MUTATED    1  3
  JAK2 WILD-TYPE 61 69
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            130 
  JAK2 MUTATED JAK2 WILD-TYPE 
             3             69 
$`JAK2 MUTATED`
TCGA-HZ-7925 TCGA-HZ-8002 TCGA-IB-7651 TCGA-IB-7885 
       20.19        12.03        19.82        41.33 

$`JAK2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  JAK2 MUTATED JAK2 WILD-TYPE 
         12.03           0.13 
  JAK2 MUTATED JAK2 WILD-TYPE 
         41.33          75.12 
  JAK2 MUTATED JAK2 WILD-TYPE 
        20.005         13.500 
[1] "12.0 - 41.3 (20.0)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.1"
D76V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  JAK2 MUTATED          0        0         0         4         0        0
  JAK2 WILD-TYPE        4        6        20        95         4        3
D76V3, multiclass
           clus
vv          JAK2 MUTATED JAK2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            4             95
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  JAK2 MUTATED     0   0     4
  JAK2 WILD-TYPE   5  13   114
D76V4, multiclass
       clus
vv      JAK2 MUTATED JAK2 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                cls
clus               0   1
  JAK2 MUTATED     0   4
  JAK2 WILD-TYPE  32 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      0    4
  JAK2 WILD-TYPE   32  100
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0            0             32
  1            4            100
[1] 2 2
[1] FALSE
D76V6, binary
                cls
clus              0  1
  JAK2 MUTATED    2  0
  JAK2 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      2    0
  JAK2 WILD-TYPE   60    3
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D76V7, binary
                cls
clus              0  1
  JAK2 MUTATED    2  2
  JAK2 WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      2    2
  JAK2 WILD-TYPE   60   72
        clus
vv       JAK2 MUTATED JAK2 WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  JAK2 MUTATED                                     4
  JAK2 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  JAK2 MUTATED                                       0
  JAK2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  JAK2 MUTATED                                                  0
  JAK2 WILD-TYPE                                                2
D76V8, multiclass
                                                  clus
vv                                                 JAK2 MUTATED JAK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, continuous
[1] "Remove cluster labels:" "JAK2 MUTATED"          
clus
  JAK2 MUTATED JAK2 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7891 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
D76V10, continuous
[1] "Remove cluster labels:" "JAK2 MUTATED"          
clus
  JAK2 MUTATED JAK2 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7891 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-YY-A8LH 
"JAK2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  JAK2 MUTATED    4  0  0  0
  JAK2 WILD-TYPE 73 48  1  3
D76V11, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  R0            4             73
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JAK2 MUTATED       0                         0     4
  JAK2 WILD-TYPE     2                         5   121
D76V13, multiclass
                           clus
vv                          JAK2 MUTATED JAK2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                cls
clus               0   1
  JAK2 MUTATED     0   4
  JAK2 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      0    4
  JAK2 WILD-TYPE    3  100
                        clus
vv                       JAK2 MUTATED JAK2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(77) Variable = COL28A1 MUTATION ANALYSIS
D77V1, survival
                   sevent
clus2                0  1
  COL28A1 MUTATED    2  3
  COL28A1 WILD-TYPE 60 69
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               129 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                3                69 
$`COL28A1 MUTATED`
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-IB-7651 TCGA-IB-7885 TCGA-YH-A8SY 
       20.19        17.03        19.82        41.33        12.76 

$`COL28A1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 
        1.02        12.89        13.84        19.50         0.13        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        66.28         0.69 

  COL28A1 MUTATED COL28A1 WILD-TYPE 
            12.76              0.13 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
            41.33             75.12 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
            19.82             13.32 
[1] "12.8 - 41.3 (19.8)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.3"
D77V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  COL28A1 MUTATED          0        0         0         4         1        0
  COL28A1 WILD-TYPE        4        6        20        95         3        3
D77V3, multiclass
           clus
vv          COL28A1 MUTATED COL28A1 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               4                95
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  COL28A1 MUTATED     0   0     5
  COL28A1 WILD-TYPE   5  13   113
D77V4, multiclass
       clus
vv      COL28A1 MUTATED COL28A1 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               5               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    0  5
  COL28A1 WILD-TYPE 32 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      0    5
  COL28A1 WILD-TYPE   32   99
   clus
vv  COL28A1 MUTATED COL28A1 WILD-TYPE
  0               0                32
  1               5                99
[1] 2 2
[1] FALSE
D77V6, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    2  0
  COL28A1 WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      2    0
  COL28A1 WILD-TYPE   60    3
   clus
vv  COL28A1 MUTATED COL28A1 WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D77V7, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    3  2
  COL28A1 WILD-TYPE 59 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      3    2
  COL28A1 WILD-TYPE   59   72
        clus
vv       COL28A1 MUTATED COL28A1 WILD-TYPE
  FEMALE               3                59
  MALE                 2                72
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COL28A1 MUTATED                                     4
  COL28A1 WILD-TYPE                                 118
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COL28A1 MUTATED                                       0
  COL28A1 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COL28A1 MUTATED                                                  0
  COL28A1 WILD-TYPE                                                2
D77V8, multiclass
                                                  clus
vv                                                 COL28A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 COL28A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, continuous
[1] "Remove cluster labels:" "COL28A1 MUTATED"       
clus
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
D77V10, continuous
[1] "Remove cluster labels:" "COL28A1 MUTATED"       
clus
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                2                37 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7891 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-YY-A8LH 
"COL28A1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  COL28A1 MUTATED    3  0  0  1
  COL28A1 WILD-TYPE 74 48  1  2
D77V11, multiclass
    clus
vv   COL28A1 MUTATED COL28A1 WILD-TYPE
  R0               3                74
  R1               0                48
  R2               0                 1
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL28A1 MUTATED       0                         1     4
  COL28A1 WILD-TYPE     2                         4   121
D77V13, multiclass
                           clus
vv                          COL28A1 MUTATED COL28A1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   4               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    0  5
  COL28A1 WILD-TYPE  3 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      0    5
  COL28A1 WILD-TYPE    3   99
                        clus
vv                       COL28A1 MUTATED COL28A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5                99
[1] 2 2
[1] FALSE

Clustering(78) Variable = KLHL20 MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2               0  1
  KLHL20 MUTATED    0  3
  KLHL20 WILD-TYPE 62 69
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              131 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3               69 
$`KLHL20 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7887 
       20.19        19.82         3.62 

$`KLHL20 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  KLHL20 MUTATED KLHL20 WILD-TYPE 
            3.62             0.13 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
           20.19            75.12 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
           19.82            13.68 
[1] "3.6 - 20.2 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2"  
D78V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KLHL20 MUTATED          0        0         0         3         0        0
  KLHL20 WILD-TYPE        4        6        20        96         4        3
D78V3, multiclass
           clus
vv          KLHL20 MUTATED KLHL20 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  KLHL20 MUTATED     0   0     3
  KLHL20 WILD-TYPE   5  13   115
D78V4, multiclass
       clus
vv      KLHL20 MUTATED KLHL20 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V5, binary
                  cls
clus                 0   1
  KLHL20 MUTATED     0   3
  KLHL20 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      0    3
  KLHL20 WILD-TYPE   32  101
   clus
vv  KLHL20 MUTATED KLHL20 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D78V6, binary
                  cls
clus                0  1
  KLHL20 MUTATED    2  0
  KLHL20 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      2    0
  KLHL20 WILD-TYPE   60    3
   clus
vv  KLHL20 MUTATED KLHL20 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D78V7, binary
                  cls
clus                0  1
  KLHL20 MUTATED    2  1
  KLHL20 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      2    1
  KLHL20 WILD-TYPE   60   73
        clus
vv       KLHL20 MUTATED KLHL20 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLHL20 MUTATED                                     3
  KLHL20 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLHL20 MUTATED                                       0
  KLHL20 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLHL20 MUTATED                                                  0
  KLHL20 WILD-TYPE                                                2
D78V8, multiclass
                                                  clus
vv                                                 KLHL20 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 KLHL20 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, continuous
[1] "Remove cluster labels:" "KLHL20 MUTATED"        
clus
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
D78V10, continuous
[1] "Remove cluster labels:" "KLHL20 MUTATED"        
clus
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  KLHL20 MUTATED    2  1  0  0
  KLHL20 WILD-TYPE 75 47  1  3
D78V11, multiclass
    clus
vv   KLHL20 MUTATED KLHL20 WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLHL20 MUTATED       0                         0     3
  KLHL20 WILD-TYPE     2                         5   122
D78V13, multiclass
                           clus
vv                          KLHL20 MUTATED KLHL20 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                  cls
clus                 0   1
  KLHL20 MUTATED     0   3
  KLHL20 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      0    3
  KLHL20 WILD-TYPE    3  101
                        clus
vv                       KLHL20 MUTATED KLHL20 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(79) Variable = WRN MUTATION ANALYSIS
D79V1, survival
               sevent
clus2            0  1
  WRN MUTATED    1  3
  WRN WILD-TYPE 61 69
  WRN MUTATED WRN WILD-TYPE 
            4           130 
  WRN MUTATED WRN WILD-TYPE 
            3            69 
$`WRN MUTATED`
TCGA-2J-AABA TCGA-FB-AAQ1 TCGA-HZ-8002 TCGA-IB-AAUR 
       19.96         4.04        12.03        11.11 

$`WRN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       34.82        23.54        15.55         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17         6.02         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  WRN MUTATED WRN WILD-TYPE 
         4.04          0.13 
  WRN MUTATED WRN WILD-TYPE 
        19.96         75.12 
  WRN MUTATED WRN WILD-TYPE 
       11.570        13.825 
[1] "4.0 - 20.0 (11.6)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.1"
D79V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WRN MUTATED          0        0         0         4         0        0
  WRN WILD-TYPE        4        6        20        95         4        3
D79V3, multiclass
           clus
vv          WRN MUTATED WRN WILD-TYPE
  STAGE IA            0             4
  STAGE IB            0             6
  STAGE IIA           0            20
  STAGE IIB           4            95
  STAGE III           0             4
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  WRN MUTATED     0   0     4
  WRN WILD-TYPE   5  13   114
D79V4, multiclass
       clus
vv      WRN MUTATED WRN WILD-TYPE
  T1              0             5
  T2              0            13
  T3+T4           4           114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V5, binary
               cls
clus              0   1
  WRN MUTATED     0   4
  WRN WILD-TYPE  32 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    4
  WRN WILD-TYPE   32  100
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           0            32
  1           4           100
[1] 2 2
[1] FALSE
D79V6, binary
               cls
clus             0  1
  WRN MUTATED    2  0
  WRN WILD-TYPE 60  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      2    0
  WRN WILD-TYPE   60    3
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           2            60
  1           0             3
[1] 2 2
[1] FALSE
D79V7, binary
               cls
clus             0  1
  WRN MUTATED    0  4
  WRN WILD-TYPE 62 70
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    4
  WRN WILD-TYPE   62   70
        clus
vv       WRN MUTATED WRN WILD-TYPE
  FEMALE           0            62
  MALE             4            70
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WRN MUTATED                                     4
  WRN WILD-TYPE                                 118
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WRN MUTATED                                       0
  WRN WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WRN MUTATED                                                  0
  WRN WILD-TYPE                                                2
D79V8, multiclass
                                                  clus
vv                                                 WRN MUTATED WRN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, continuous
[1] "Remove cluster labels:" "WRN MUTATED"           
clus
  WRN MUTATED WRN WILD-TYPE 
            1            47 
   TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO    TCGA-2J-AABV 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB    TCGA-3A-A9IX 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-F2-A8YN    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM    TCGA-FB-A78T 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-H6-A45N    TCGA-HZ-A77Q 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-HZ-A8P0    TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649    TCGA-IB-7651 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891    TCGA-IB-8126 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU    TCGA-LB-A7SX 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP    TCGA-US-A774 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-YY-A8LH 
"WRN WILD-TYPE" "WRN WILD-TYPE" 
D79V10, continuous
               vv
clus            R0 R1 R2 RX
  WRN MUTATED    1  3  0  0
  WRN WILD-TYPE 76 45  1  3
D79V11, multiclass
    clus
vv   WRN MUTATED WRN WILD-TYPE
  R0           1            76
  R1           3            45
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WRN MUTATED       0                         0     4
  WRN WILD-TYPE     2                         5   121
D79V13, multiclass
                           clus
vv                          WRN MUTATED WRN WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
               cls
clus              0   1
  WRN MUTATED     0   3
  WRN WILD-TYPE   3 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    3
  WRN WILD-TYPE    3  101
                        clus
vv                       WRN MUTATED WRN WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           3           101
[1] 2 2
[1] FALSE

Clustering(80) Variable = P2RY1 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2              0  1
  P2RY1 MUTATED    2  3
  P2RY1 WILD-TYPE 60 69
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             129 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              3              69 
$`P2RY1 MUTATED`
TCGA-3A-A9IB TCGA-F2-A8YN TCGA-IB-7651 TCGA-OE-A75W TCGA-XD-AAUL 
        7.36        17.00        19.82         8.78        13.32 

$`P2RY1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98         7.66        19.27         3.12         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YB-A89D 
       14.14         0.39        13.81        12.99        12.03        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  P2RY1 MUTATED P2RY1 WILD-TYPE 
           7.36            0.13 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
          19.82           75.12 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
          13.32           13.81 
[1] "7.4 - 19.8 (13.3)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.4"
D80V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  P2RY1 MUTATED          0        0         3         2         0        0
  P2RY1 WILD-TYPE        4        6        17        97         4        3
D80V3, multiclass
           clus
vv          P2RY1 MUTATED P2RY1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             3              17
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  P2RY1 MUTATED     0   0     5
  P2RY1 WILD-TYPE   5  13   113
D80V4, multiclass
       clus
vv      P2RY1 MUTATED P2RY1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V5, binary
                 cls
clus                0   1
  P2RY1 MUTATED     3   2
  P2RY1 WILD-TYPE  29 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    2
  P2RY1 WILD-TYPE   29  102
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              29
  1             2             102
[1] 2 2
[1] FALSE
D80V6, binary
                 cls
clus               0  1
  P2RY1 MUTATED    3  0
  P2RY1 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    0
  P2RY1 WILD-TYPE   59    3
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus               0  1
  P2RY1 MUTATED    2  3
  P2RY1 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      2    3
  P2RY1 WILD-TYPE   60   71
        clus
vv       P2RY1 MUTATED P2RY1 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  P2RY1 MUTATED                                     5
  P2RY1 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  P2RY1 MUTATED                                       0
  P2RY1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  P2RY1 MUTATED                                                  0
  P2RY1 WILD-TYPE                                                2
D80V8, multiclass
                                                  clus
vv                                                 P2RY1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 P2RY1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, continuous
D80V10, continuous
                 vv
clus              R0 R1 R2 RX
  P2RY1 MUTATED    4  1  0  0
  P2RY1 WILD-TYPE 73 47  1  3
D80V11, multiclass
    clus
vv   P2RY1 MUTATED P2RY1 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  P2RY1 MUTATED       0                         0     5
  P2RY1 WILD-TYPE     2                         5   120
D80V13, multiclass
                           clus
vv                          P2RY1 MUTATED P2RY1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                 cls
clus               0  1
  P2RY1 MUTATED    0  5
  P2RY1 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      0    5
  P2RY1 WILD-TYPE    3   99
                        clus
vv                       P2RY1 MUTATED P2RY1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(81) Variable = RBL2 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2             0  1
  RBL2 MUTATED    2  2
  RBL2 WILD-TYPE 60 70
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            130 
  RBL2 MUTATED RBL2 WILD-TYPE 
             2             70 
$`RBL2 MUTATED`
TCGA-HZ-8001 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-AAUU 
       23.21        12.95        19.82         8.05 

$`RBL2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 
       21.60         5.26        10.85         1.08         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.40         9.44        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  RBL2 MUTATED RBL2 WILD-TYPE 
          8.05           0.13 
  RBL2 MUTATED RBL2 WILD-TYPE 
         23.21          75.12 
  RBL2 MUTATED RBL2 WILD-TYPE 
        16.385         13.745 
[1] "8.1 - 23.2 (16.4)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D81V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBL2 MUTATED          0        0         0         2         1        1
  RBL2 WILD-TYPE        4        6        20        97         3        2
D81V3, multiclass
           clus
vv          RBL2 MUTATED RBL2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            2             97
  STAGE III            1              3
  STAGE IV             1              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  RBL2 MUTATED     0   0     4
  RBL2 WILD-TYPE   5  13   114
D81V4, multiclass
       clus
vv      RBL2 MUTATED RBL2 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V5, binary
                cls
clus               0   1
  RBL2 MUTATED     1   3
  RBL2 WILD-TYPE  31 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      1    3
  RBL2 WILD-TYPE   31  101
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0            1             31
  1            3            101
[1] 2 2
[1] FALSE
D81V6, binary
                cls
clus              0  1
  RBL2 MUTATED    2  1
  RBL2 WILD-TYPE 60  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      2    1
  RBL2 WILD-TYPE   60    2
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0            2             60
  1            1              2
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus              0  1
  RBL2 MUTATED    2  2
  RBL2 WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      2    2
  RBL2 WILD-TYPE   60   72
        clus
vv       RBL2 MUTATED RBL2 WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBL2 MUTATED                                     4
  RBL2 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBL2 MUTATED                                       0
  RBL2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBL2 MUTATED                                                  0
  RBL2 WILD-TYPE                                                2
D81V8, multiclass
                                                  clus
vv                                                 RBL2 MUTATED RBL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, continuous
D81V10, continuous
[1] "Remove cluster labels:" "RBL2 MUTATED"          
clus
  RBL2 MUTATED RBL2 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
    TCGA-YY-A8LH 
"RBL2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RBL2 MUTATED    3  1  0  0
  RBL2 WILD-TYPE 74 47  1  3
D81V11, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0            3             74
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBL2 MUTATED       0                         0     4
  RBL2 WILD-TYPE     2                         5   121
D81V13, multiclass
                           clus
vv                          RBL2 MUTATED RBL2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                cls
clus               0   1
  RBL2 MUTATED     0   4
  RBL2 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      0    4
  RBL2 WILD-TYPE    3  100
                        clus
vv                       RBL2 MUTATED RBL2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(82) Variable = BCLAF1 MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2               0  1
  BCLAF1 MUTATED    1  5
  BCLAF1 WILD-TYPE 61 67
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              128 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               5               67 
$`BCLAF1 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IB TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-A5SQ TCGA-M8-A5N4 
       22.49         7.36        12.95        19.82         7.20        19.20 

$`BCLAF1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       53.00        23.61        20.84        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        12.00        15.85        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE 
        8.05        12.92        12.46        10.29         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            7.20             0.13 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           22.49            75.12 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          16.075           13.745 
[1] "7.2 - 22.5 (16.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.7"
D82V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BCLAF1 MUTATED          0        1         1         3         0        1
  BCLAF1 WILD-TYPE        4        5        19        96         4        2
D82V3, multiclass
           clus
vv          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               1                5
  STAGE IIA              1               19
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               1                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  BCLAF1 MUTATED     0   1     5
  BCLAF1 WILD-TYPE   5  12   113
D82V4, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V5, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     2   4
  BCLAF1 WILD-TYPE  30 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      2    4
  BCLAF1 WILD-TYPE   30  100
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              2               30
  1              4              100
[1] 2 2
[1] FALSE
D82V6, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    4  1
  BCLAF1 WILD-TYPE 58  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      4    1
  BCLAF1 WILD-TYPE   58    2
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              4               58
  1              1                2
[1] 2 2
[1] FALSE
D82V7, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    5  1
  BCLAF1 WILD-TYPE 57 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      5    1
  BCLAF1 WILD-TYPE   57   73
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              5               57
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCLAF1 MUTATED                                     6
  BCLAF1 WILD-TYPE                                 116
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCLAF1 MUTATED                                       0
  BCLAF1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCLAF1 MUTATED                                                  0
  BCLAF1 WILD-TYPE                                                2
D82V8, multiclass
                                                  clus
vv                                                 BCLAF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 BCLAF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V9, continuous
D82V10, continuous
                  vv
clus               R0 R1 R2 RX
  BCLAF1 MUTATED    4  2  0  0
  BCLAF1 WILD-TYPE 73 46  1  3
D82V11, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  R0              4               73
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED       0                         0     5
  BCLAF1 WILD-TYPE     2                         5   120
D82V13, multiclass
                           clus
vv                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     0   4
  BCLAF1 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0    4
  BCLAF1 WILD-TYPE    3  100
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(83) Variable = MORF4L1 MUTATION ANALYSIS
D83V1, survival
                   sevent
clus2                0  1
  MORF4L1 MUTATED    1  2
  MORF4L1 WILD-TYPE 61 70
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               131 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                2                70 
$`MORF4L1 MUTATED`
TCGA-2L-AAQJ TCGA-IB-7885 TCGA-PZ-A5RE 
       12.95        41.33        15.45 

$`MORF4L1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29        19.20         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            12.95              0.13 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            41.33             75.12 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            15.45             13.68 
[1] "12.9 - 41.3 (15.4)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "1.2"
D83V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MORF4L1 MUTATED          0        0         0         2         1        0
  MORF4L1 WILD-TYPE        4        6        20        97         3        3
D83V3, multiclass
           clus
vv          MORF4L1 MUTATED MORF4L1 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               2                97
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  MORF4L1 MUTATED     0   0     3
  MORF4L1 WILD-TYPE   5  13   115
D83V4, multiclass
       clus
vv      MORF4L1 MUTATED MORF4L1 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V5, binary
                   cls
clus                  0   1
  MORF4L1 MUTATED     1   2
  MORF4L1 WILD-TYPE  31 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      1    2
  MORF4L1 WILD-TYPE   31  102
   clus
vv  MORF4L1 MUTATED MORF4L1 WILD-TYPE
  0               1                31
  1               2               102
[1] 2 2
[1] FALSE
D83V6, binary
                   cls
clus                 0  1
  MORF4L1 MUTATED    1  0
  MORF4L1 WILD-TYPE 61  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      1    0
  MORF4L1 WILD-TYPE   61    3
   clus
vv  MORF4L1 MUTATED MORF4L1 WILD-TYPE
  0               1                61
  1               0                 3
[1] 2 2
[1] FALSE
D83V7, binary
                   cls
clus                 0  1
  MORF4L1 MUTATED    3  0
  MORF4L1 WILD-TYPE 59 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      3    0
  MORF4L1 WILD-TYPE   59   74
        clus
vv       MORF4L1 MUTATED MORF4L1 WILD-TYPE
  FEMALE               3                59
  MALE                 0                74
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MORF4L1 MUTATED                                     3
  MORF4L1 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MORF4L1 MUTATED                                       0
  MORF4L1 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MORF4L1 MUTATED                                                  0
  MORF4L1 WILD-TYPE                                                2
D83V8, multiclass
                                                  clus
vv                                                 MORF4L1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 MORF4L1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V9, continuous
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                1                47 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7886        TCGA-IB-7887 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-YY-A8LH 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
D83V10, continuous
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                1                38 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7886 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  MORF4L1 MUTATED    1  1  0  0
  MORF4L1 WILD-TYPE 76 47  1  3
D83V11, multiclass
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                2               127 
       TCGA-2J-AAB1        TCGA-2J-AAB4        TCGA-2J-AAB6        TCGA-2J-AAB8 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-2J-AAB9        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-2J-AABH        TCGA-2J-AABK        TCGA-2J-AABO        TCGA-2J-AABR 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-2J-AABU        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-2L-AAQI        TCGA-2L-AAQL        TCGA-3A-A9I5        TCGA-3A-A9I7 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IC        TCGA-3A-A9IH 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-3A-A9IU        TCGA-3A-A9IX        TCGA-3A-A9IZ        TCGA-3A-A9J0 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-F2-6879        TCGA-F2-A44G        TCGA-F2-A44H        TCGA-F2-A7TX 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPU        TCGA-FB-AAPY        TCGA-FB-AAPZ 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-FB-AAQ0        TCGA-FB-AAQ1        TCGA-FB-AAQ2        TCGA-FB-AAQ3 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-7919        TCGA-HZ-7922        TCGA-HZ-7925 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-7926        TCGA-HZ-8001        TCGA-HZ-8002        TCGA-HZ-8003 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-8005        TCGA-HZ-8315        TCGA-HZ-8317        TCGA-HZ-8519 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-8636        TCGA-HZ-8637        TCGA-HZ-A49G        TCGA-HZ-A49H 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-A49I        TCGA-HZ-A4BH        TCGA-HZ-A4BK        TCGA-HZ-A77O 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HZ-A77P        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7645        TCGA-IB-7646        TCGA-IB-7647 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7652        TCGA-IB-7886 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7888        TCGA-IB-7889        TCGA-IB-7890 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-7893        TCGA-IB-7897        TCGA-IB-8126 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SO        TCGA-IB-A5SP        TCGA-IB-A5SQ 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A5ST        TCGA-IB-A6UF        TCGA-IB-A6UG 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A7LX        TCGA-IB-A7M4        TCGA-IB-AAUM        TCGA-IB-AAUN 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUO        TCGA-IB-AAUP        TCGA-IB-AAUQ        TCGA-IB-AAUR 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-LB-A8F3        TCGA-LB-A9Q5        TCGA-M8-A5N4        TCGA-OE-A75W 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-Q3-A5QY        TCGA-Q3-AA2A        TCGA-RB-A7B8        TCGA-RB-AA9M 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RO        TCGA-S4-A8RP        TCGA-US-A774 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-US-A776        TCGA-US-A779        TCGA-US-A77E        TCGA-US-A77G 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-XD-AAUG        TCGA-XD-AAUH        TCGA-XD-AAUI        TCGA-XD-AAUL 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-YB-A89D        TCGA-YY-A8LH        TCGA-Z5-AAPL 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
D83V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MORF4L1 MUTATED       0                         0     3
  MORF4L1 WILD-TYPE     2                         5   122
D83V13, multiclass
                           clus
vv                          MORF4L1 MUTATED MORF4L1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V14, binary
                   cls
clus                  0   1
  MORF4L1 MUTATED     0   2
  MORF4L1 WILD-TYPE   3 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      0    2
  MORF4L1 WILD-TYPE    3  102
                        clus
vv                       MORF4L1 MUTATED MORF4L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               2               102
[1] 2 2
[1] FALSE

Clustering(84) Variable = SEPHS2 MUTATION ANALYSIS
D84V1, survival
                  sevent
clus2               0  1
  SEPHS2 MUTATED    3  2
  SEPHS2 WILD-TYPE 59 70
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              129 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               2               70 
$`SEPHS2 MUTATED`
TCGA-3A-A9IX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-IB-A5SS TCGA-RB-A7B8 
       34.09        17.00        14.76        15.12        15.32 

$`SEPHS2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98         7.66        19.27         3.12         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       24.07        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-S4-A8RM 
        8.78        15.45        13.68         3.12         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           14.76             0.13 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           34.09            75.12 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           15.32            12.99 
[1] "14.8 - 34.1 (15.3)" "0.1 - 75.1 (13.0)" 
[1] "hr=" "1.7"
D84V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SEPHS2 MUTATED          1        1         1         2         0        0
  SEPHS2 WILD-TYPE        3        5        19        97         4        3
D84V3, multiclass
           clus
vv          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               1                5
  STAGE IIA              1               19
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  SEPHS2 MUTATED     1   1     3
  SEPHS2 WILD-TYPE   4  12   115
D84V4, multiclass
       clus
vv      SEPHS2 MUTATED SEPHS2 WILD-TYPE
  T1                 1                4
  T2                 1               12
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V5, binary
                  cls
clus                 0   1
  SEPHS2 MUTATED     3   2
  SEPHS2 WILD-TYPE  29 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    2
  SEPHS2 WILD-TYPE   29  102
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               29
  1              2              102
[1] 2 2
[1] FALSE
D84V6, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    3  0
  SEPHS2 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    0
  SEPHS2 WILD-TYPE   59    3
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D84V7, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    2  3
  SEPHS2 WILD-TYPE 60 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      2    3
  SEPHS2 WILD-TYPE   60   71
        clus
vv       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  FEMALE              2               60
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEPHS2 MUTATED                                     4
  SEPHS2 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEPHS2 MUTATED                                       1
  SEPHS2 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEPHS2 MUTATED                                                  0
  SEPHS2 WILD-TYPE                                                2
D84V8, multiclass
                                                  clus
vv                                                 SEPHS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 SEPHS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V9, continuous
D84V10, continuous
                  vv
clus               R0 R1 R2 RX
  SEPHS2 MUTATED    4  1  0  0
  SEPHS2 WILD-TYPE 73 47  1  3
D84V11, multiclass
    clus
vv   SEPHS2 MUTATED SEPHS2 WILD-TYPE
  R0              4               73
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEPHS2 MUTATED       0                         0     5
  SEPHS2 WILD-TYPE     2                         5   120
D84V13, multiclass
                           clus
vv                          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V14, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    0  5
  SEPHS2 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      0    5
  SEPHS2 WILD-TYPE    3   99
                        clus
vv                       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(85) Variable = HELZ MUTATION ANALYSIS
D85V1, survival
                sevent
clus2             0  1
  HELZ MUTATED    0  5
  HELZ WILD-TYPE 62 67
  HELZ MUTATED HELZ WILD-TYPE 
             5            129 
  HELZ MUTATED HELZ WILD-TYPE 
             5             67 
$`HELZ MUTATED`
TCGA-FB-AAPU TCGA-HZ-7925 TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
       12.53        20.19        12.95        15.35        19.82 

$`HELZ WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  HELZ MUTATED HELZ WILD-TYPE 
         12.53           0.13 
  HELZ MUTATED HELZ WILD-TYPE 
         20.19          75.12 
  HELZ MUTATED HELZ WILD-TYPE 
         15.35          13.68 
[1] "12.5 - 20.2 (15.3)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "1.9"
D85V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HELZ MUTATED          0        0         1         3         0        1
  HELZ WILD-TYPE        4        6        19        96         4        2
D85V3, multiclass
           clus
vv          HELZ MUTATED HELZ WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            1             19
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             1              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  HELZ MUTATED     0   0     5
  HELZ WILD-TYPE   5  13   113
D85V4, multiclass
       clus
vv      HELZ MUTATED HELZ WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V5, binary
                cls
clus               0   1
  HELZ MUTATED     1   4
  HELZ WILD-TYPE  31 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      1    4
  HELZ WILD-TYPE   31  100
   clus
vv  HELZ MUTATED HELZ WILD-TYPE
  0            1             31
  1            4            100
[1] 2 2
[1] FALSE
D85V6, binary
                cls
clus              0  1
  HELZ MUTATED    2  1
  HELZ WILD-TYPE 60  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      2    1
  HELZ WILD-TYPE   60    2
   clus
vv  HELZ MUTATED HELZ WILD-TYPE
  0            2             60
  1            1              2
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus              0  1
  HELZ MUTATED    4  1
  HELZ WILD-TYPE 58 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      4    1
  HELZ WILD-TYPE   58   73
        clus
vv       HELZ MUTATED HELZ WILD-TYPE
  FEMALE            4             58
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HELZ MUTATED                                     5
  HELZ WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HELZ MUTATED                                       0
  HELZ WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HELZ MUTATED                                                  0
  HELZ WILD-TYPE                                                2
D85V8, multiclass
                                                  clus
vv                                                 HELZ MUTATED HELZ WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V9, continuous
D85V10, continuous
                vv
clus             R0 R1 R2 RX
  HELZ MUTATED    2  3  0  0
  HELZ WILD-TYPE 75 45  1  3
D85V11, multiclass
    clus
vv   HELZ MUTATED HELZ WILD-TYPE
  R0            2             75
  R1            3             45
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HELZ MUTATED       1                         0     3
  HELZ WILD-TYPE     1                         5   122
D85V13, multiclass
                           clus
vv                          HELZ MUTATED HELZ WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V14, binary
                cls
clus               0   1
  HELZ MUTATED     0   4
  HELZ WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      0    4
  HELZ WILD-TYPE    3  100
                        clus
vv                       HELZ MUTATED HELZ WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(86) Variable = DOCK8 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2              0  1
  DOCK8 MUTATED    2  2
  DOCK8 WILD-TYPE 60 70
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              4             130 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              2              70 
$`DOCK8 MUTATED`
TCGA-2J-AAB4 TCGA-3A-A9IB TCGA-IB-7651 TCGA-IB-8127 
       23.97         7.36        19.82        17.16 

$`DOCK8 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       53.00        23.61        20.84        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  DOCK8 MUTATED DOCK8 WILD-TYPE 
           7.36            0.13 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          23.97           75.12 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          18.49           13.50 
[1] "7.4 - 24.0 (18.5)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.3"
D86V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DOCK8 MUTATED          0        0         0         4         0        0
  DOCK8 WILD-TYPE        4        6        20        95         4        3
D86V3, multiclass
           clus
vv          DOCK8 MUTATED DOCK8 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  DOCK8 MUTATED     0   1     3
  DOCK8 WILD-TYPE   5  12   115
D86V4, multiclass
       clus
vv      DOCK8 MUTATED DOCK8 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V5, binary
                 cls
clus                0   1
  DOCK8 MUTATED     0   4
  DOCK8 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      0    4
  DOCK8 WILD-TYPE   32  100
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D86V6, binary
                 cls
clus               0  1
  DOCK8 MUTATED    3  0
  DOCK8 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      3    0
  DOCK8 WILD-TYPE   59    3
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D86V7, binary
                 cls
clus               0  1
  DOCK8 MUTATED    2  2
  DOCK8 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      2    2
  DOCK8 WILD-TYPE   60   72
        clus
vv       DOCK8 MUTATED DOCK8 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DOCK8 MUTATED                                     3
  DOCK8 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DOCK8 MUTATED                                       1
  DOCK8 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DOCK8 MUTATED                                                  0
  DOCK8 WILD-TYPE                                                2
D86V8, multiclass
                                                  clus
vv                                                 DOCK8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DOCK8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V9, continuous
D86V10, continuous
                 vv
clus              R0 R1 R2 RX
  DOCK8 MUTATED    3  1  0  0
  DOCK8 WILD-TYPE 74 47  1  3
D86V11, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOCK8 MUTATED       0                         0     4
  DOCK8 WILD-TYPE     2                         5   121
D86V13, multiclass
                           clus
vv                          DOCK8 MUTATED DOCK8 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V14, binary
                 cls
clus                0   1
  DOCK8 MUTATED     0   3
  DOCK8 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      0    3
  DOCK8 WILD-TYPE    3  101
                        clus
vv                       DOCK8 MUTATED DOCK8 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(87) Variable = KLK13 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2              0  1
  KLK13 MUTATED    2  3
  KLK13 WILD-TYPE 60 69
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             129 
  KLK13 MUTATED KLK13 WILD-TYPE 
              3              69 
$`KLK13 MUTATED`
TCGA-2L-AAQE TCGA-FB-A78T TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-A5SS 
       22.49        12.43         1.08        19.82        15.12 

$`KLK13 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
        2.47        17.16        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  KLK13 MUTATED KLK13 WILD-TYPE 
           1.08            0.13 
  KLK13 MUTATED KLK13 WILD-TYPE 
          22.49           75.12 
  KLK13 MUTATED KLK13 WILD-TYPE 
          15.12           13.68 
[1] "1.1 - 22.5 (15.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D87V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KLK13 MUTATED          0        0         0         5         0        0
  KLK13 WILD-TYPE        4        6        20        94         4        3
D87V3, multiclass
           clus
vv          KLK13 MUTATED KLK13 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KLK13 MUTATED     0   0     5
  KLK13 WILD-TYPE   5  13   113
D87V4, multiclass
       clus
vv      KLK13 MUTATED KLK13 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V5, binary
                 cls
clus               0  1
  KLK13 MUTATED    0  5
  KLK13 WILD-TYPE 32 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    5
  KLK13 WILD-TYPE   32   99
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             0              32
  1             5              99
[1] 2 2
[1] FALSE
D87V6, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  0
  KLK13 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    0
  KLK13 WILD-TYPE   58    3
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             4              58
  1             0               3
[1] 2 2
[1] FALSE
D87V7, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  1
  KLK13 WILD-TYPE 58 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    1
  KLK13 WILD-TYPE   58   73
        clus
vv       KLK13 MUTATED KLK13 WILD-TYPE
  FEMALE             4              58
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK13 MUTATED                                     4
  KLK13 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK13 MUTATED                                       1
  KLK13 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK13 MUTATED                                                  0
  KLK13 WILD-TYPE                                                2
D87V8, multiclass
                                                  clus
vv                                                 KLK13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KLK13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V9, continuous
D87V10, continuous
                 vv
clus              R0 R1 R2 RX
  KLK13 MUTATED    5  0  0  0
  KLK13 WILD-TYPE 72 48  1  3
D87V11, multiclass
    clus
vv   KLK13 MUTATED KLK13 WILD-TYPE
  R0             5              72
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK13 MUTATED       0                         0     5
  KLK13 WILD-TYPE     2                         5   120
D87V13, multiclass
                           clus
vv                          KLK13 MUTATED KLK13 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V14, binary
                 cls
clus                0   1
  KLK13 MUTATED     0   4
  KLK13 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    4
  KLK13 WILD-TYPE    3  100
                        clus
vv                       KLK13 MUTATED KLK13 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(88) Variable = OXR1 MUTATION ANALYSIS
D88V1, survival
                sevent
clus2             0  1
  OXR1 MUTATED    0  4
  OXR1 WILD-TYPE 62 68
  OXR1 MUTATED OXR1 WILD-TYPE 
             4            130 
  OXR1 MUTATED OXR1 WILD-TYPE 
             4             68 
$`OXR1 MUTATED`
TCGA-3A-A9IZ TCGA-HZ-7925 TCGA-HZ-7926 TCGA-IB-7649 
       10.13        20.19        17.03        15.35 

$`OXR1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        34.09        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8002 
       12.89        13.84        19.50         0.13        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  OXR1 MUTATED OXR1 WILD-TYPE 
         10.13           0.13 
  OXR1 MUTATED OXR1 WILD-TYPE 
         20.19          75.12 
  OXR1 MUTATED OXR1 WILD-TYPE 
         16.19          13.50 
[1] "10.1 - 20.2 (16.2)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.9"
D88V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OXR1 MUTATED          0        0         0         4         0        0
  OXR1 WILD-TYPE        4        6        20        95         4        3
D88V3, multiclass
           clus
vv          OXR1 MUTATED OXR1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            4             95
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  OXR1 MUTATED     0   0     4
  OXR1 WILD-TYPE   5  13   114
D88V4, multiclass
       clus
vv      OXR1 MUTATED OXR1 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V5, binary
                cls
clus               0   1
  OXR1 MUTATED     0   4
  OXR1 WILD-TYPE  32 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      0    4
  OXR1 WILD-TYPE   32  100
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            0             32
  1            4            100
[1] 2 2
[1] FALSE
D88V6, binary
                cls
clus              0  1
  OXR1 MUTATED    1  0
  OXR1 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    0
  OXR1 WILD-TYPE   61    3
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D88V7, binary
                cls
clus              0  1
  OXR1 MUTATED    1  3
  OXR1 WILD-TYPE 61 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    3
  OXR1 WILD-TYPE   61   71
        clus
vv       OXR1 MUTATED OXR1 WILD-TYPE
  FEMALE            1             61
  MALE              3             71
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OXR1 MUTATED                                     4
  OXR1 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OXR1 MUTATED                                       0
  OXR1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OXR1 MUTATED                                                  0
  OXR1 WILD-TYPE                                                2
D88V8, multiclass
                                                  clus
vv                                                 OXR1 MUTATED OXR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V9, continuous
[1] "Remove cluster labels:" "OXR1 MUTATED"          
clus
  OXR1 MUTATED OXR1 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
D88V10, continuous
[1] "Remove cluster labels:" "OXR1 MUTATED"          
clus
  OXR1 MUTATED OXR1 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  OXR1 MUTATED    1  2  0  1
  OXR1 WILD-TYPE 76 46  1  2
D88V11, multiclass
    clus
vv   OXR1 MUTATED OXR1 WILD-TYPE
  R0            1             76
  R1            2             46
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXR1 MUTATED       0                         1     2
  OXR1 WILD-TYPE     2                         4   123
D88V13, multiclass
                           clus
vv                          OXR1 MUTATED OXR1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                2            123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V14, binary
                cls
clus               0   1
  OXR1 MUTATED     1   2
  OXR1 WILD-TYPE   2 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    2
  OXR1 WILD-TYPE    2  102
                        clus
vv                       OXR1 MUTATED OXR1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            2            102
[1] 2 2
[1] FALSE

Clustering(89) Variable = OR52D1 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2               0  1
  OR52D1 MUTATED    3  1
  OR52D1 WILD-TYPE 59 71
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              130 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               1               71 
$`OR52D1 MUTATED`
TCGA-FB-A4P6 TCGA-HZ-8519 TCGA-HZ-A4BK TCGA-IB-7651 
       11.93        14.93        21.60        19.82 

$`OR52D1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77O 
       17.92        21.70        16.14        10.13         6.38         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  OR52D1 MUTATED OR52D1 WILD-TYPE 
           11.93             0.13 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
           21.60            75.12 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
          17.375           13.500 
[1] "11.9 - 21.6 (17.4)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "2.4"
D89V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR52D1 MUTATED          1        0         0         3         0        0
  OR52D1 WILD-TYPE        3        6        20        96         4        3
D89V3, multiclass
           clus
vv          OR52D1 MUTATED OR52D1 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  OR52D1 MUTATED     1   0     3
  OR52D1 WILD-TYPE   4  13   115
D89V4, multiclass
       clus
vv      OR52D1 MUTATED OR52D1 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V5, binary
                  cls
clus                 0   1
  OR52D1 MUTATED     1   3
  OR52D1 WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    3
  OR52D1 WILD-TYPE   31  101
   clus
vv  OR52D1 MUTATED OR52D1 WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D89V6, binary
                  cls
clus                0  1
  OR52D1 MUTATED    1  0
  OR52D1 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    0
  OR52D1 WILD-TYPE   61    3
   clus
vv  OR52D1 MUTATED OR52D1 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D89V7, binary
                  cls
clus                0  1
  OR52D1 MUTATED    1  3
  OR52D1 WILD-TYPE 61 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    3
  OR52D1 WILD-TYPE   61   71
        clus
vv       OR52D1 MUTATED OR52D1 WILD-TYPE
  FEMALE              1               61
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR52D1 MUTATED                                     2
  OR52D1 WILD-TYPE                                 120
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR52D1 MUTATED                                       2
  OR52D1 WILD-TYPE                                     9
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR52D1 MUTATED                                                  0
  OR52D1 WILD-TYPE                                                2
D89V8, multiclass
                                                  clus
vv                                                 OR52D1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 OR52D1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V9, continuous
[1] "Remove cluster labels:" "OR52D1 MUTATED"        
clus
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
D89V10, continuous
[1] "Remove cluster labels:" "OR52D1 MUTATED"        
clus
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A5VM 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-YY-A8LH 
"OR52D1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OR52D1 MUTATED    2  1  0  0
  OR52D1 WILD-TYPE 75 47  1  3
D89V11, multiclass
    clus
vv   OR52D1 MUTATED OR52D1 WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR52D1 MUTATED       0                         0     4
  OR52D1 WILD-TYPE     2                         5   121
D89V13, multiclass
                           clus
vv                          OR52D1 MUTATED OR52D1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V14, binary
                  cls
clus                 0   1
  OR52D1 MUTATED     0   4
  OR52D1 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      0    4
  OR52D1 WILD-TYPE    3  100
                        clus
vv                       OR52D1 MUTATED OR52D1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(90) Variable = CSTF2T MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2               0  1
  CSTF2T MUTATED    1  2
  CSTF2T WILD-TYPE 61 70
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              131 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               2               70 
$`CSTF2T MUTATED`
TCGA-HZ-7925 TCGA-IB-7897 TCGA-IB-A6UF 
       20.19        15.98        21.90 

$`CSTF2T WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
       21.30         3.85         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        15.12        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CSTF2T MUTATED CSTF2T WILD-TYPE 
           15.98             0.13 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
           21.90            75.12 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
           20.19            13.32 
[1] "16.0 - 21.9 (20.2)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.1"
D90V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CSTF2T MUTATED          0        0         0         3         0        0
  CSTF2T WILD-TYPE        4        6        20        96         4        3
D90V3, multiclass
           clus
vv          CSTF2T MUTATED CSTF2T WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CSTF2T MUTATED     0   0     3
  CSTF2T WILD-TYPE   5  13   115
D90V4, multiclass
       clus
vv      CSTF2T MUTATED CSTF2T WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V5, binary
                  cls
clus                 0   1
  CSTF2T MUTATED     0   3
  CSTF2T WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      0    3
  CSTF2T WILD-TYPE   32  101
   clus
vv  CSTF2T MUTATED CSTF2T WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D90V6, binary
                  cls
clus                0  1
  CSTF2T MUTATED    2  0
  CSTF2T WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      2    0
  CSTF2T WILD-TYPE   60    3
   clus
vv  CSTF2T MUTATED CSTF2T WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D90V7, binary
                  cls
clus                0  1
  CSTF2T MUTATED    1  2
  CSTF2T WILD-TYPE 61 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      1    2
  CSTF2T WILD-TYPE   61   72
        clus
vv       CSTF2T MUTATED CSTF2T WILD-TYPE
  FEMALE              1               61
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CSTF2T MUTATED                                     3
  CSTF2T WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CSTF2T MUTATED                                       0
  CSTF2T WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CSTF2T MUTATED                                                  0
  CSTF2T WILD-TYPE                                                2
D90V8, multiclass
                                                  clus
vv                                                 CSTF2T MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CSTF2T WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V9, continuous
[1] "Remove cluster labels:" "CSTF2T MUTATED"        
clus
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
D90V10, continuous
[1] "Remove cluster labels:" "CSTF2T MUTATED"        
clus
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-7886       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CSTF2T MUTATED    2  1  0  0
  CSTF2T WILD-TYPE 75 47  1  3
D90V11, multiclass
    clus
vv   CSTF2T MUTATED CSTF2T WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSTF2T MUTATED       0                         0     3
  CSTF2T WILD-TYPE     2                         5   122
D90V13, multiclass
                           clus
vv                          CSTF2T MUTATED CSTF2T WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V14, binary
                  cls
clus                 0   1
  CSTF2T MUTATED     0   3
  CSTF2T WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      0    3
  CSTF2T WILD-TYPE    3  101
                        clus
vv                       CSTF2T MUTATED CSTF2T WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(91) Variable = AP3B1 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2              0  1
  AP3B1 MUTATED    2  2
  AP3B1 WILD-TYPE 60 70
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             130 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              2              70 
$`AP3B1 MUTATED`
TCGA-HZ-8001 TCGA-IB-7651 TCGA-IB-7887 TCGA-S4-A8RO 
       23.21        19.82         3.62        17.26 

$`AP3B1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        9.40        21.24        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  AP3B1 MUTATED AP3B1 WILD-TYPE 
           3.62            0.13 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          23.21           75.12 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          18.54           13.50 
[1] "3.6 - 23.2 (18.5)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.3"
D91V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AP3B1 MUTATED          0        0         0         3         1        0
  AP3B1 WILD-TYPE        4        6        20        96         3        3
D91V3, multiclass
           clus
vv          AP3B1 MUTATED AP3B1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  AP3B1 MUTATED     0   0     4
  AP3B1 WILD-TYPE   5  13   114
D91V4, multiclass
       clus
vv      AP3B1 MUTATED AP3B1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V5, binary
                 cls
clus                0   1
  AP3B1 MUTATED     1   3
  AP3B1 WILD-TYPE  31 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      1    3
  AP3B1 WILD-TYPE   31  101
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0             1              31
  1             3             101
[1] 2 2
[1] FALSE
D91V6, binary
                 cls
clus               0  1
  AP3B1 MUTATED    2  0
  AP3B1 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      2    0
  AP3B1 WILD-TYPE   60    3
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D91V7, binary
                 cls
clus               0  1
  AP3B1 MUTATED    3  1
  AP3B1 WILD-TYPE 59 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      3    1
  AP3B1 WILD-TYPE   59   73
        clus
vv       AP3B1 MUTATED AP3B1 WILD-TYPE
  FEMALE             3              59
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AP3B1 MUTATED                                     4
  AP3B1 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AP3B1 MUTATED                                       0
  AP3B1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AP3B1 MUTATED                                                  0
  AP3B1 WILD-TYPE                                                2
D91V8, multiclass
                                                  clus
vv                                                 AP3B1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 AP3B1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V9, continuous
[1] "Remove cluster labels:" "AP3B1 MUTATED"         
clus
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
D91V10, continuous
[1] "Remove cluster labels:" "AP3B1 MUTATED"         
clus
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  AP3B1 MUTATED    2  2  0  0
  AP3B1 WILD-TYPE 75 46  1  3
D91V11, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  R0             2              75
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AP3B1 MUTATED       0                         0     4
  AP3B1 WILD-TYPE     2                         5   121
D91V13, multiclass
                           clus
vv                          AP3B1 MUTATED AP3B1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V14, binary
                 cls
clus                0   1
  AP3B1 MUTATED     0   4
  AP3B1 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      0    4
  AP3B1 WILD-TYPE    3  100
                        clus
vv                       AP3B1 MUTATED AP3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(92) Variable = OMA1 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2             0  1
  OMA1 MUTATED    0  3
  OMA1 WILD-TYPE 62 69
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            131 
  OMA1 MUTATED OMA1 WILD-TYPE 
             3             69 
$`OMA1 MUTATED`
TCGA-HZ-8005 TCGA-IB-7651 TCGA-IB-7887 
        3.95        19.82         3.62 

$`OMA1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  OMA1 MUTATED OMA1 WILD-TYPE 
          3.62           0.13 
  OMA1 MUTATED OMA1 WILD-TYPE 
         19.82          75.12 
  OMA1 MUTATED OMA1 WILD-TYPE 
          3.95          13.81 
[1] "3.6 - 19.8 (4.0)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.7"
D92V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OMA1 MUTATED          0        0         0         3         0        0
  OMA1 WILD-TYPE        4        6        20        96         4        3
D92V3, multiclass
           clus
vv          OMA1 MUTATED OMA1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  OMA1 MUTATED     0   0     3
  OMA1 WILD-TYPE   5  13   115
D92V4, multiclass
       clus
vv      OMA1 MUTATED OMA1 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V5, binary
                cls
clus               0   1
  OMA1 MUTATED     0   3
  OMA1 WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      0    3
  OMA1 WILD-TYPE   32  101
   clus
vv  OMA1 MUTATED OMA1 WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D92V6, binary
                cls
clus              0  1
  OMA1 MUTATED    2  0
  OMA1 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      2    0
  OMA1 WILD-TYPE   60    3
   clus
vv  OMA1 MUTATED OMA1 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D92V7, binary
                cls
clus              0  1
  OMA1 MUTATED    2  1
  OMA1 WILD-TYPE 60 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      2    1
  OMA1 WILD-TYPE   60   73
        clus
vv       OMA1 MUTATED OMA1 WILD-TYPE
  FEMALE            2             60
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OMA1 MUTATED                                     3
  OMA1 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OMA1 MUTATED                                       0
  OMA1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OMA1 MUTATED                                                  0
  OMA1 WILD-TYPE                                                2
D92V8, multiclass
                                                  clus
vv                                                 OMA1 MUTATED OMA1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V9, continuous
[1] "Remove cluster labels:" "OMA1 MUTATED"          
clus
  OMA1 MUTATED OMA1 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
D92V10, continuous
[1] "Remove cluster labels:" "OMA1 MUTATED"          
clus
  OMA1 MUTATED OMA1 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  OMA1 MUTATED    1  2  0  0
  OMA1 WILD-TYPE 76 46  1  3
D92V11, multiclass
    clus
vv   OMA1 MUTATED OMA1 WILD-TYPE
  R0            1             76
  R1            2             46
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OMA1 MUTATED       0                         0     3
  OMA1 WILD-TYPE     2                         5   122
D92V13, multiclass
                           clus
vv                          OMA1 MUTATED OMA1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V14, binary
                cls
clus               0   1
  OMA1 MUTATED     0   3
  OMA1 WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      0    3
  OMA1 WILD-TYPE    3  101
                        clus
vv                       OMA1 MUTATED OMA1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(93) Variable = IYD MUTATION ANALYSIS
D93V1, survival
               sevent
clus2            0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 59 69
  IYD MUTATED IYD WILD-TYPE 
            6           128 
  IYD MUTATED IYD WILD-TYPE 
            3            69 
$`IYD MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-HZ-A49I TCGA-LB-A8F3 TCGA-US-A779 TCGA-Z5-AAPL 
       23.54        15.55        10.13        12.46        16.80         0.69 

$`IYD WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       12.53        34.82         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.92        21.70        16.14         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.40         9.44         8.05        12.92        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        27.75        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

  IYD MUTATED IYD WILD-TYPE 
         0.69          0.13 
  IYD MUTATED IYD WILD-TYPE 
        23.54         75.12 
  IYD MUTATED IYD WILD-TYPE 
       14.005        13.745 
[1] "0.7 - 23.5 (14.0)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1"  
D93V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IYD MUTATED          0        0         3         3         0        0
  IYD WILD-TYPE        4        6        17        96         4        3
D93V3, multiclass
           clus
vv          IYD MUTATED IYD WILD-TYPE
  STAGE IA            0             4
  STAGE IB            0             6
  STAGE IIA           3            17
  STAGE IIB           3            96
  STAGE III           0             4
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  IYD MUTATED     0   1     5
  IYD WILD-TYPE   5  12   113
D93V4, multiclass
       clus
vv      IYD MUTATED IYD WILD-TYPE
  T1              0             5
  T2              1            12
  T3+T4           5           113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V5, binary
               cls
clus              0   1
  IYD MUTATED     3   3
  IYD WILD-TYPE  29 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    3
  IYD WILD-TYPE   29  101
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           3            29
  1           3           101
[1] 2 2
[1] FALSE
D93V6, binary
               cls
clus             0  1
  IYD MUTATED    1  0
  IYD WILD-TYPE 61  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      1    0
  IYD WILD-TYPE   61    3
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           1            61
  1           0             3
[1] 2 2
[1] FALSE
D93V7, binary
               cls
clus             0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 59 71
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    3
  IYD WILD-TYPE   59   71
        clus
vv       IYD MUTATED IYD WILD-TYPE
  FEMALE           3            59
  MALE             3            71
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IYD MUTATED                                     6
  IYD WILD-TYPE                                 116
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IYD MUTATED                                       0
  IYD WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IYD MUTATED                                                  0
  IYD WILD-TYPE                                                2
D93V8, multiclass
                                                  clus
vv                                                 IYD MUTATED IYD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        6           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V9, continuous
D93V10, continuous
               vv
clus            R0 R1 R2 RX
  IYD MUTATED    5  1  0  0
  IYD WILD-TYPE 72 47  1  3
D93V11, multiclass
    clus
vv   IYD MUTATED IYD WILD-TYPE
  R0           5            72
  R1           1            47
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IYD MUTATED       0                         1     5
  IYD WILD-TYPE     2                         4   120
D93V13, multiclass
                           clus
vv                          IYD MUTATED IYD WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                               5           120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V14, binary
               cls
clus             0  1
  IYD MUTATED    0  6
  IYD WILD-TYPE  3 98
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      0    6
  IYD WILD-TYPE    3   98
                        clus
vv                       IYD MUTATED IYD WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           6            98
[1] 2 2
[1] FALSE

Clustering(94) Variable = PRSS3 MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2              0  1
  PRSS3 MUTATED    1  2
  PRSS3 WILD-TYPE 61 70
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             131 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              2              70 
$`PRSS3 MUTATED`
TCGA-3A-A9IU TCGA-FB-A5VM TCGA-LB-A9Q5 
       15.06        14.76        10.29 

$`PRSS3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  PRSS3 MUTATED PRSS3 WILD-TYPE 
          10.29            0.13 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
          15.06           75.12 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
          14.76           13.68 
[1] "10.3 - 15.1 (14.8)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "1.7"
D94V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PRSS3 MUTATED          0        1         0         2         0        0
  PRSS3 WILD-TYPE        4        5        20        97         4        3
D94V3, multiclass
           clus
vv          PRSS3 MUTATED PRSS3 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             0              20
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PRSS3 MUTATED     0   1     2
  PRSS3 WILD-TYPE   5  12   116
D94V4, multiclass
       clus
vv      PRSS3 MUTATED PRSS3 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             2             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V5, binary
                 cls
clus                0   1
  PRSS3 MUTATED     1   2
  PRSS3 WILD-TYPE  31 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    2
  PRSS3 WILD-TYPE   31  102
   clus
vv  PRSS3 MUTATED PRSS3 WILD-TYPE
  0             1              31
  1             2             102
[1] 2 2
[1] FALSE
D94V6, binary
                 cls
clus               0  1
  PRSS3 MUTATED    1  0
  PRSS3 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    0
  PRSS3 WILD-TYPE   61    3
   clus
vv  PRSS3 MUTATED PRSS3 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D94V7, binary
                 cls
clus               0  1
  PRSS3 MUTATED    1  2
  PRSS3 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    2
  PRSS3 WILD-TYPE   61   72
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRSS3 MUTATED                                     3
  PRSS3 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRSS3 MUTATED                                       0
  PRSS3 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRSS3 MUTATED                                                  0
  PRSS3 WILD-TYPE                                                2
D94V8, multiclass
                                                  clus
vv                                                 PRSS3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PRSS3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V9, continuous
[1] "Remove cluster labels:" "PRSS3 MUTATED"         
clus
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A78T      TCGA-FB-AAPS 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
D94V10, continuous
[1] "Remove cluster labels:" "PRSS3 MUTATED"         
clus
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-OE-A75W 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-YY-A8LH 
"PRSS3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRSS3 MUTATED    3  0  0  0
  PRSS3 WILD-TYPE 74 48  1  3
D94V11, multiclass
    clus
vv   PRSS3 MUTATED PRSS3 WILD-TYPE
  R0             3              74
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRSS3 MUTATED       0                         0     3
  PRSS3 WILD-TYPE     2                         5   122
D94V13, multiclass
                           clus
vv                          PRSS3 MUTATED PRSS3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V14, binary
                 cls
clus                0   1
  PRSS3 MUTATED     0   3
  PRSS3 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      0    3
  PRSS3 WILD-TYPE    3  101
                        clus
vv                       PRSS3 MUTATED PRSS3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(95) Variable = COBL MUTATION ANALYSIS
D95V1, survival
                sevent
clus2             0  1
  COBL MUTATED    2  4
  COBL WILD-TYPE 60 68
  COBL MUTATED COBL WILD-TYPE 
             6            128 
  COBL MUTATED COBL WILD-TYPE 
             4             68 
$`COBL MUTATED`
TCGA-FB-A545 TCGA-HZ-7925 TCGA-HZ-8519 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-AAUS 
       24.07        20.19        14.93        19.82         4.04         7.40 

$`COBL WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        11.93        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8636 
       12.03         0.69         3.95         9.83        12.43        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       21.90        15.35        23.80        41.33         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUT TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  COBL MUTATED COBL WILD-TYPE 
          4.04           0.13 
  COBL MUTATED COBL WILD-TYPE 
         24.07          75.12 
  COBL MUTATED COBL WILD-TYPE 
        17.375         13.500 
[1] "4.0 - 24.1 (17.4)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.2"
D95V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  COBL MUTATED          1        0         0         5         0        0
  COBL WILD-TYPE        3        6        20        94         4        3
D95V3, multiclass
           clus
vv          COBL MUTATED COBL WILD-TYPE
  STAGE IA             1              3
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  COBL MUTATED     1   0     5
  COBL WILD-TYPE   4  13   113
D95V4, multiclass
       clus
vv      COBL MUTATED COBL WILD-TYPE
  T1               1              4
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V5, binary
                cls
clus              0  1
  COBL MUTATED    1  5
  COBL WILD-TYPE 31 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      1    5
  COBL WILD-TYPE   31   99
   clus
vv  COBL MUTATED COBL WILD-TYPE
  0            1             31
  1            5             99
[1] 2 2
[1] FALSE
D95V6, binary
                cls
clus              0  1
  COBL MUTATED    4  0
  COBL WILD-TYPE 58  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      4    0
  COBL WILD-TYPE   58    3
   clus
vv  COBL MUTATED COBL WILD-TYPE
  0            4             58
  1            0              3
[1] 2 2
[1] FALSE
D95V7, binary
                cls
clus              0  1
  COBL MUTATED    3  3
  COBL WILD-TYPE 59 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      3    3
  COBL WILD-TYPE   59   71
        clus
vv       COBL MUTATED COBL WILD-TYPE
  FEMALE            3             59
  MALE              3             71
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COBL MUTATED                                     5
  COBL WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COBL MUTATED                                       1
  COBL WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COBL MUTATED                                                  0
  COBL WILD-TYPE                                                2
D95V8, multiclass
                                                  clus
vv                                                 COBL MUTATED COBL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V9, continuous
D95V10, continuous
                vv
clus             R0 R1 R2 RX
  COBL MUTATED    3  2  0  0
  COBL WILD-TYPE 74 46  1  3
D95V11, multiclass
    clus
vv   COBL MUTATED COBL WILD-TYPE
  R0            3             74
  R1            2             46
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COBL MUTATED       0                         0     6
  COBL WILD-TYPE     2                         5   119
D95V13, multiclass
                           clus
vv                          COBL MUTATED COBL WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V14, binary
                cls
clus              0  1
  COBL MUTATED    0  6
  COBL WILD-TYPE  3 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      0    6
  COBL WILD-TYPE    3   98
                        clus
vv                       COBL MUTATED COBL WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6             98
[1] 2 2
[1] FALSE

Clustering(96) Variable = SORT1 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2              0  1
  SORT1 MUTATED    3  2
  SORT1 WILD-TYPE 59 70
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             129 
  SORT1 MUTATED SORT1 WILD-TYPE 
              2              70 
$`SORT1 MUTATED`
TCGA-F2-A44H TCGA-HZ-8001 TCGA-IB-7651 TCGA-IB-7887 TCGA-LB-A8F3 
       19.27        23.21        19.82         3.62        12.46 

$`SORT1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74        10.98         7.66         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.44         8.05        12.92        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  SORT1 MUTATED SORT1 WILD-TYPE 
           3.62            0.13 
  SORT1 MUTATED SORT1 WILD-TYPE 
          23.21           75.12 
  SORT1 MUTATED SORT1 WILD-TYPE 
          19.27           13.68 
[1] "3.6 - 23.2 (19.3)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.5"
D96V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SORT1 MUTATED          0        0         2         2         1        0
  SORT1 WILD-TYPE        4        6        18        97         3        3
D96V3, multiclass
           clus
vv          SORT1 MUTATED SORT1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             2              97
  STAGE III             1               3
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SORT1 MUTATED     0   0     5
  SORT1 WILD-TYPE   5  13   113
D96V4, multiclass
       clus
vv      SORT1 MUTATED SORT1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V5, binary
                 cls
clus                0   1
  SORT1 MUTATED     3   2
  SORT1 WILD-TYPE  29 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    2
  SORT1 WILD-TYPE   29  102
   clus
vv  SORT1 MUTATED SORT1 WILD-TYPE
  0             3              29
  1             2             102
[1] 2 2
[1] FALSE
D96V6, binary
                 cls
clus               0  1
  SORT1 MUTATED    3  0
  SORT1 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    0
  SORT1 WILD-TYPE   59    3
   clus
vv  SORT1 MUTATED SORT1 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D96V7, binary
                 cls
clus               0  1
  SORT1 MUTATED    3  2
  SORT1 WILD-TYPE 59 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    2
  SORT1 WILD-TYPE   59   72
        clus
vv       SORT1 MUTATED SORT1 WILD-TYPE
  FEMALE             3              59
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORT1 MUTATED                                     5
  SORT1 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORT1 MUTATED                                       0
  SORT1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORT1 MUTATED                                                  0
  SORT1 WILD-TYPE                                                2
D96V8, multiclass
                                                  clus
vv                                                 SORT1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SORT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V9, continuous
[1] "Remove cluster labels:" "SORT1 MUTATED"         
clus
  SORT1 MUTATED SORT1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
D96V10, continuous
[1] "Remove cluster labels:" "SORT1 MUTATED"         
clus
  SORT1 MUTATED SORT1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SORT1 MUTATED    4  1  0  0
  SORT1 WILD-TYPE 73 47  1  3
D96V11, multiclass
    clus
vv   SORT1 MUTATED SORT1 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORT1 MUTATED       0                         1     4
  SORT1 WILD-TYPE     2                         4   121
D96V13, multiclass
                           clus
vv                          SORT1 MUTATED SORT1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V14, binary
                 cls
clus               0  1
  SORT1 MUTATED    0  5
  SORT1 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      0    5
  SORT1 WILD-TYPE    3   99
                        clus
vv                       SORT1 MUTATED SORT1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              99
[1] 2 2
[1] FALSE

Clustering(97) Variable = SSBP3 MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2              0  1
  SSBP3 MUTATED    0  3
  SSBP3 WILD-TYPE 62 69
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             131 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3              69 
$`SSBP3 MUTATED`
TCGA-FB-AAQ2 TCGA-IB-A5SO TCGA-OE-A75W 
        5.03        12.00         8.78 

$`SSBP3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 
       12.53        34.82        23.54        15.55         4.04         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP 
       21.30         3.85        15.98         2.47        17.16        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29        19.20        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SSBP3 MUTATED SSBP3 WILD-TYPE 
           5.03            0.13 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          12.00           75.12 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
           8.78           13.84 
[1] "5.0 - 12.0 (8.8)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "5"  
D97V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SSBP3 MUTATED          0        0         1         2         0        0
  SSBP3 WILD-TYPE        4        6        19        97         4        3
D97V3, multiclass
           clus
vv          SSBP3 MUTATED SSBP3 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SSBP3 MUTATED     0   0     3
  SSBP3 WILD-TYPE   5  13   115
D97V4, multiclass
       clus
vv      SSBP3 MUTATED SSBP3 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V5, binary
                 cls
clus                0   1
  SSBP3 MUTATED     1   2
  SSBP3 WILD-TYPE  31 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   31  102
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             1              31
  1             2             102
[1] 2 2
[1] FALSE
D97V6, binary
                 cls
clus               0  1
  SSBP3 MUTATED    2  0
  SSBP3 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    0
  SSBP3 WILD-TYPE   60    3
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D97V7, binary
                 cls
clus               0  1
  SSBP3 MUTATED    1  2
  SSBP3 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   61   72
        clus
vv       SSBP3 MUTATED SSBP3 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SSBP3 MUTATED                                     3
  SSBP3 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SSBP3 MUTATED                                       0
  SSBP3 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SSBP3 MUTATED                                                  0
  SSBP3 WILD-TYPE                                                2
D97V8, multiclass
                                                  clus
vv                                                 SSBP3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SSBP3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V9, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
D97V10, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SSBP3 MUTATED    2  1  0  0
  SSBP3 WILD-TYPE 75 47  1  3
D97V11, multiclass
    clus
vv   SSBP3 MUTATED SSBP3 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSBP3 MUTATED       0                         0     3
  SSBP3 WILD-TYPE     2                         5   122
D97V13, multiclass
                           clus
vv                          SSBP3 MUTATED SSBP3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V14, binary
                 cls
clus                0   1
  SSBP3 MUTATED     0   2
  SSBP3 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      0    2
  SSBP3 WILD-TYPE    3  102
                        clus
vv                       SSBP3 MUTATED SSBP3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(98) Variable = GPSM2 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2              0  1
  GPSM2 MUTATED    0  3
  GPSM2 WILD-TYPE 62 69
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             131 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3              69 
$`GPSM2 MUTATED`
TCGA-F2-A44G TCGA-FB-A545 TCGA-IB-7886 
        7.66        24.07         4.04 

$`GPSM2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74        10.98        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  GPSM2 MUTATED GPSM2 WILD-TYPE 
           4.04            0.13 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          24.07           75.12 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
           7.66           13.81 
[1] "4.0 - 24.1 (7.7)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.1"
D98V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPSM2 MUTATED          0        0         0         3         0        0
  GPSM2 WILD-TYPE        4        6        20        96         4        3
D98V3, multiclass
           clus
vv          GPSM2 MUTATED GPSM2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  GPSM2 MUTATED     0   0     3
  GPSM2 WILD-TYPE   5  13   115
D98V4, multiclass
       clus
vv      GPSM2 MUTATED GPSM2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V5, binary
                 cls
clus                0   1
  GPSM2 MUTATED     0   3
  GPSM2 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      0    3
  GPSM2 WILD-TYPE   32  101
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D98V6, binary
                 cls
clus               0  1
  GPSM2 MUTATED    3  0
  GPSM2 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      3    0
  GPSM2 WILD-TYPE   59    3
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D98V7, binary
                 cls
clus               0  1
  GPSM2 MUTATED    2  1
  GPSM2 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      2    1
  GPSM2 WILD-TYPE   60   73
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPSM2 MUTATED                                     3
  GPSM2 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPSM2 MUTATED                                       0
  GPSM2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPSM2 MUTATED                                                  0
  GPSM2 WILD-TYPE                                                2
D98V8, multiclass
                                                  clus
vv                                                 GPSM2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 GPSM2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V9, continuous
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7887 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
D98V10, continuous
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  GPSM2 MUTATED    0  2  0  0
  GPSM2 WILD-TYPE 77 46  1  3
D98V11, multiclass
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              2             127 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-2J-AAB9      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-2J-AABH      TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-2J-AABU      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-2L-AAQI      TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I5 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-3A-A9I7      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-3A-A9IH      TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-3A-A9J0      TCGA-F2-6879      TCGA-F2-A44H      TCGA-F2-A7TX 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A4P5      TCGA-FB-A5VM      TCGA-FB-A78T 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY      TCGA-FB-AAPZ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-7919      TCGA-HZ-7922      TCGA-HZ-7925 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7645      TCGA-IB-7646      TCGA-IB-7647 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7890 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-7893      TCGA-IB-7897      TCGA-IB-8126 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-M8-A5N4      TCGA-OE-A75W 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP      TCGA-US-A774 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E      TCGA-US-A77G 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XD-AAUL 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
D98V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPSM2 MUTATED       0                         0     3
  GPSM2 WILD-TYPE     2                         5   122
D98V13, multiclass
                           clus
vv                          GPSM2 MUTATED GPSM2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V14, binary
                 cls
clus                0   1
  GPSM2 MUTATED     0   3
  GPSM2 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      0    3
  GPSM2 WILD-TYPE    3  101
                        clus
vv                       GPSM2 MUTATED GPSM2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(99) Variable = EEF2 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  EEF2 MUTATED    0  5
  EEF2 WILD-TYPE 62 67
  EEF2 MUTATED EEF2 WILD-TYPE 
             5            129 
  EEF2 MUTATED EEF2 WILD-TYPE 
             5             67 
$`EEF2 MUTATED`
TCGA-2L-AAQL TCGA-F2-A44G TCGA-FB-AAQ3 TCGA-IB-7651 TCGA-US-A774 
        9.60         7.66         1.02        19.82        22.85 

$`EEF2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  EEF2 MUTATED EEF2 WILD-TYPE 
          1.02           0.13 
  EEF2 MUTATED EEF2 WILD-TYPE 
         22.85          75.12 
  EEF2 MUTATED EEF2 WILD-TYPE 
          9.60          13.81 
[1] "1.0 - 22.9 (9.6)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.4"
D99V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  EEF2 MUTATED          0        0         0         5         0        0
  EEF2 WILD-TYPE        4        6        20        94         4        3
D99V3, multiclass
           clus
vv          EEF2 MUTATED EEF2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  EEF2 MUTATED     0   0     5
  EEF2 WILD-TYPE   5  13   113
D99V4, multiclass
       clus
vv      EEF2 MUTATED EEF2 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V5, binary
                cls
clus              0  1
  EEF2 MUTATED    0  5
  EEF2 WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      0    5
  EEF2 WILD-TYPE   32   99
   clus
vv  EEF2 MUTATED EEF2 WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D99V6, binary
                cls
clus              0  1
  EEF2 MUTATED    2  0
  EEF2 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      2    0
  EEF2 WILD-TYPE   60    3
   clus
vv  EEF2 MUTATED EEF2 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D99V7, binary
                cls
clus              0  1
  EEF2 MUTATED    4  1
  EEF2 WILD-TYPE 58 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      4    1
  EEF2 WILD-TYPE   58   73
        clus
vv       EEF2 MUTATED EEF2 WILD-TYPE
  FEMALE            4             58
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EEF2 MUTATED                                     5
  EEF2 WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EEF2 MUTATED                                       0
  EEF2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EEF2 MUTATED                                                  0
  EEF2 WILD-TYPE                                                2
D99V8, multiclass
                                                  clus
vv                                                 EEF2 MUTATED EEF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V9, continuous
[1] "Remove cluster labels:" "EEF2 MUTATED"          
clus
  EEF2 MUTATED EEF2 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
D99V10, continuous
[1] "Remove cluster labels:" "EEF2 MUTATED"          
clus
  EEF2 MUTATED EEF2 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-XD-AAUI     TCGA-XD-AAUL 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-YY-A8LH 
"EEF2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  EEF2 MUTATED    3  1  0  1
  EEF2 WILD-TYPE 74 47  1  2
D99V11, multiclass
    clus
vv   EEF2 MUTATED EEF2 WILD-TYPE
  R0            3             74
  R1            1             47
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EEF2 MUTATED       0                         0     5
  EEF2 WILD-TYPE     2                         5   120
D99V13, multiclass
                           clus
vv                          EEF2 MUTATED EEF2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V14, binary
                cls
clus               0   1
  EEF2 MUTATED     0   4
  EEF2 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      0    4
  EEF2 WILD-TYPE    3  100
                        clus
vv                       EEF2 MUTATED EEF2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(100) Variable = ZACN MUTATION ANALYSIS
D100V1, survival
                sevent
clus2             0  1
  ZACN MUTATED    1  2
  ZACN WILD-TYPE 61 70
  ZACN MUTATED ZACN WILD-TYPE 
             3            131 
  ZACN MUTATED ZACN WILD-TYPE 
             2             70 
$`ZACN MUTATED`
TCGA-IB-A5SQ TCGA-US-A774 TCGA-US-A776 
        7.20        22.85        27.75 

$`ZACN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ZACN MUTATED ZACN WILD-TYPE 
          7.20           0.13 
  ZACN MUTATED ZACN WILD-TYPE 
         27.75          75.12 
  ZACN MUTATED ZACN WILD-TYPE 
         22.85          13.68 
[1] "7.2 - 27.8 (22.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.3"
D100V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZACN MUTATED          0        1         1         1         0        0
  ZACN WILD-TYPE        4        5        19        98         4        3
D100V3, multiclass
           clus
vv          ZACN MUTATED ZACN WILD-TYPE
  STAGE IA             0              4
  STAGE IB             1              5
  STAGE IIA            1             19
  STAGE IIB            1             98
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  ZACN MUTATED     0   1     2
  ZACN WILD-TYPE   5  12   116
D100V4, multiclass
       clus
vv      ZACN MUTATED ZACN WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            2            116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V5, binary
                cls
clus               0   1
  ZACN MUTATED     2   1
  ZACN WILD-TYPE  30 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      2    1
  ZACN WILD-TYPE   30  103
   clus
vv  ZACN MUTATED ZACN WILD-TYPE
  0            2             30
  1            1            103
[1] 2 2
[1] FALSE
D100V6, binary
                cls
clus              0  1
  ZACN MUTATED    1  0
  ZACN WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      1    0
  ZACN WILD-TYPE   61    3
   clus
vv  ZACN MUTATED ZACN WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D100V7, binary
                cls
clus              0  1
  ZACN MUTATED    2  1
  ZACN WILD-TYPE 60 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      2    1
  ZACN WILD-TYPE   60   73
        clus
vv       ZACN MUTATED ZACN WILD-TYPE
  FEMALE            2             60
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZACN MUTATED                                     2
  ZACN WILD-TYPE                                 120
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZACN MUTATED                                       0
  ZACN WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZACN MUTATED                                                  1
  ZACN WILD-TYPE                                                1
D100V8, multiclass
                                                  clus
vv                                                 ZACN MUTATED ZACN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V9, continuous
[1] "Remove cluster labels:" "ZACN MUTATED"          
clus
  ZACN MUTATED ZACN WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-XD-AAUL     TCGA-YY-A8LH 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
D100V10, continuous
[1] "Remove cluster labels:" "ZACN MUTATED"          
clus
  ZACN MUTATED ZACN WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-7886     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-XD-AAUI 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ZACN MUTATED    3  0  0  0
  ZACN WILD-TYPE 74 48  1  3
D100V11, multiclass
    clus
vv   ZACN MUTATED ZACN WILD-TYPE
  R0            3             74
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZACN MUTATED       0                         0     3
  ZACN WILD-TYPE     2                         5   122
D100V13, multiclass
                           clus
vv                          ZACN MUTATED ZACN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V14, binary
                cls
clus               0   1
  ZACN MUTATED     0   3
  ZACN WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      0    3
  ZACN WILD-TYPE    3  101
                        clus
vv                       ZACN MUTATED ZACN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(101) Variable = ZMYM2 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2              0  1
  ZMYM2 MUTATED    0  3
  ZMYM2 WILD-TYPE 62 69
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             131 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3              69 
$`ZMYM2 MUTATED`
TCGA-F2-6879 TCGA-HZ-8005 TCGA-IB-7651 
       10.98         3.95        19.82 

$`ZMYM2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
           3.95            0.13 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          19.82           75.12 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          10.98           13.81 
[1] "4.0 - 19.8 (11.0)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.8"
D101V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZMYM2 MUTATED          0        0         0         3         0        0
  ZMYM2 WILD-TYPE        4        6        20        96         4        3
D101V3, multiclass
           clus
vv          ZMYM2 MUTATED ZMYM2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ZMYM2 MUTATED     0   0     3
  ZMYM2 WILD-TYPE   5  13   115
D101V4, multiclass
       clus
vv      ZMYM2 MUTATED ZMYM2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V5, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0   3
  ZMYM2 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0    3
  ZMYM2 WILD-TYPE   32  101
   clus
vv  ZMYM2 MUTATED ZMYM2 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D101V6, binary
                 cls
clus               0  1
  ZMYM2 MUTATED    2  0
  ZMYM2 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      2    0
  ZMYM2 WILD-TYPE   60    3
   clus
vv  ZMYM2 MUTATED ZMYM2 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D101V7, binary
                 cls
clus               0  1
  ZMYM2 MUTATED    1  2
  ZMYM2 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      1    2
  ZMYM2 WILD-TYPE   61   72
        clus
vv       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYM2 MUTATED                                     2
  ZMYM2 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYM2 MUTATED                                       1
  ZMYM2 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYM2 MUTATED                                                  0
  ZMYM2 WILD-TYPE                                                2
D101V8, multiclass
                                                  clus
vv                                                 ZMYM2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZMYM2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V9, continuous
[1] "Remove cluster labels:" "ZMYM2 MUTATED"         
clus
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
D101V10, continuous
[1] "Remove cluster labels:" "ZMYM2 MUTATED"         
clus
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZMYM2 MUTATED    2  1  0  0
  ZMYM2 WILD-TYPE 75 47  1  3
D101V11, multiclass
    clus
vv   ZMYM2 MUTATED ZMYM2 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM2 MUTATED       0                         0     3
  ZMYM2 WILD-TYPE     2                         5   122
D101V13, multiclass
                           clus
vv                          ZMYM2 MUTATED ZMYM2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V14, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0   2
  ZMYM2 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0    2
  ZMYM2 WILD-TYPE    3  102
                        clus
vv                       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(102) Variable = GSN MUTATION ANALYSIS
D102V1, survival
               sevent
clus2            0  1
  GSN MUTATED    2  2
  GSN WILD-TYPE 60 70
  GSN MUTATED GSN WILD-TYPE 
            4           130 
  GSN MUTATED GSN WILD-TYPE 
            2            70 
$`GSN MUTATED`
TCGA-FB-A545 TCGA-HZ-A49H TCGA-IB-7651 TCGA-M8-A5N4 
       24.07        16.14        19.82        19.20 

$`GSN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        11.93        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        21.70        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  GSN MUTATED GSN WILD-TYPE 
        16.14          0.13 
  GSN MUTATED GSN WILD-TYPE 
        24.07         75.12 
  GSN MUTATED GSN WILD-TYPE 
       19.510        13.155 
[1] "16.1 - 24.1 (19.5)" "0.1 - 75.1 (13.2)" 
[1] "hr=" "1.6"
D102V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GSN MUTATED          0        0         1         3         0        0
  GSN WILD-TYPE        4        6        19        96         4        3
D102V3, multiclass
           clus
vv          GSN MUTATED GSN WILD-TYPE
  STAGE IA            0             4
  STAGE IB            0             6
  STAGE IIA           1            19
  STAGE IIB           3            96
  STAGE III           0             4
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  GSN MUTATED     0   0     4
  GSN WILD-TYPE   5  13   114
D102V4, multiclass
       clus
vv      GSN MUTATED GSN WILD-TYPE
  T1              0             5
  T2              0            13
  T3+T4           4           114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V5, binary
               cls
clus              0   1
  GSN MUTATED     1   3
  GSN WILD-TYPE  31 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      1    3
  GSN WILD-TYPE   31  101
   clus
vv  GSN MUTATED GSN WILD-TYPE
  0           1            31
  1           3           101
[1] 2 2
[1] FALSE
D102V6, binary
               cls
clus             0  1
  GSN MUTATED    3  0
  GSN WILD-TYPE 59  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      3    0
  GSN WILD-TYPE   59    3
   clus
vv  GSN MUTATED GSN WILD-TYPE
  0           3            59
  1           0             3
[1] 2 2
[1] FALSE
D102V7, binary
               cls
clus             0  1
  GSN MUTATED    4  0
  GSN WILD-TYPE 58 74
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      4    0
  GSN WILD-TYPE   58   74
        clus
vv       GSN MUTATED GSN WILD-TYPE
  FEMALE           4            58
  MALE             0            74
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GSN MUTATED                                     4
  GSN WILD-TYPE                                 118
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GSN MUTATED                                       0
  GSN WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GSN MUTATED                                                  0
  GSN WILD-TYPE                                                2
D102V8, multiclass
                                                  clus
vv                                                 GSN MUTATED GSN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V9, continuous
[1] "Remove cluster labels:" "GSN MUTATED"           
clus
  GSN MUTATED GSN WILD-TYPE 
            1            47 
   TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-FB-A78T    TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-H6-A45N 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891    TCGA-IB-8126 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU    TCGA-LB-A7SX 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP    TCGA-US-A774 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-YY-A8LH 
"GSN WILD-TYPE" "GSN WILD-TYPE" 
D102V10, continuous
[1] "Remove cluster labels:" "GSN MUTATED"           
clus
  GSN MUTATED GSN WILD-TYPE 
            1            38 
   TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO    TCGA-3A-A9IB 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM    TCGA-FB-A78T 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-HZ-A77Q    TCGA-HZ-A8P0 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649    TCGA-IB-7885    TCGA-IB-7886 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-7891    TCGA-IB-8126    TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-LB-A7SX    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-US-A774 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-XD-AAUI    TCGA-XD-AAUL    TCGA-YY-A8LH 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  GSN MUTATED    2  1  0  0
  GSN WILD-TYPE 75 47  1  3
D102V11, multiclass
    clus
vv   GSN MUTATED GSN WILD-TYPE
  R0           2            75
  R1           1            47
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GSN MUTATED       0                         0     3
  GSN WILD-TYPE     2                         5   122
D102V13, multiclass
                           clus
vv                          GSN MUTATED GSN WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V14, binary
               cls
clus              0   1
  GSN MUTATED     0   3
  GSN WILD-TYPE   3 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      0    3
  GSN WILD-TYPE    3  101
                        clus
vv                       GSN MUTATED GSN WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           3           101
[1] 2 2
[1] FALSE

Clustering(103) Variable = TGFBR1 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2               0  1
  TGFBR1 MUTATED    4  4
  TGFBR1 WILD-TYPE 58 68
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              126 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               4               68 
$`TGFBR1 MUTATED`
TCGA-3E-AAAY TCGA-FB-A4P5 TCGA-H6-8124 TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUU 
       75.12         5.88        12.89        19.82        12.00         8.05 
TCGA-LB-A9Q5 TCGA-YY-A8LH 
       10.29        66.28 

$`TGFBR1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       28.73        15.06        34.09        10.13        12.39        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P6 
       10.98         7.66        19.27         3.12        17.00        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N 
       23.54        15.55         4.04         5.03         1.02        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.99        12.03        13.32        11.51        12.76         0.69 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            5.88             0.13 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
           75.12            71.74 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          12.445           13.825 
[1] "5.9 - 75.1 (12.4)" "0.1 - 71.7 (13.8)"
[1] "hr=" "1.6"
D103V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TGFBR1 MUTATED          0        0         0         8         0        0
  TGFBR1 WILD-TYPE        4        6        20        91         4        3
D103V3, multiclass
           clus
vv          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              8               91
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TGFBR1 MUTATED     0   0     8
  TGFBR1 WILD-TYPE   5  13   110
D103V4, multiclass
       clus
vv      TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              8              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V5, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    0  8
  TGFBR1 WILD-TYPE 32 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      0    8
  TGFBR1 WILD-TYPE   32   96
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              0               32
  1              8               96
[1] 2 2
[1] FALSE
D103V6, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    4  0
  TGFBR1 WILD-TYPE 58  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      4    0
  TGFBR1 WILD-TYPE   58    3
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              4               58
  1              0                3
[1] 2 2
[1] FALSE
D103V7, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    5  3
  TGFBR1 WILD-TYPE 57 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      5    3
  TGFBR1 WILD-TYPE   57   71
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  FEMALE              5               57
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR1 MUTATED                                     8
  TGFBR1 WILD-TYPE                                 114
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR1 MUTATED                                       0
  TGFBR1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR1 MUTATED                                                  0
  TGFBR1 WILD-TYPE                                                2
D103V8, multiclass
                                                  clus
vv                                                 TGFBR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TGFBR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           114
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V9, continuous
D103V10, continuous
                  vv
clus               R0 R1 R2 RX
  TGFBR1 MUTATED    7  0  0  0
  TGFBR1 WILD-TYPE 70 48  1  3
D103V11, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0              7               70
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR1 MUTATED       0                         0     8
  TGFBR1 WILD-TYPE     2                         5   117
D103V13, multiclass
                           clus
vv                          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V14, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    0  7
  TGFBR1 WILD-TYPE  3 97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      0    7
  TGFBR1 WILD-TYPE    3   97
                        clus
vv                       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7               97
[1] 2 2
[1] FALSE

Clustering(104) Variable = MLPH MUTATION ANALYSIS
D104V1, survival
                sevent
clus2             0  1
  MLPH MUTATED    2  1
  MLPH WILD-TYPE 60 71
  MLPH MUTATED MLPH WILD-TYPE 
             3            131 
  MLPH MUTATED MLPH WILD-TYPE 
             1             71 
$`MLPH MUTATED`
TCGA-FB-A4P6 TCGA-FB-AAPS TCGA-IB-7651 
       11.93         7.50        19.82 

$`MLPH WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
        5.88        24.07        14.76        12.43        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  MLPH MUTATED MLPH WILD-TYPE 
          7.50           0.13 
  MLPH MUTATED MLPH WILD-TYPE 
         19.82          75.12 
  MLPH MUTATED MLPH WILD-TYPE 
         11.93          13.81 
[1] "7.5 - 19.8 (11.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.2"
D104V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MLPH MUTATED          0        0         0         3         0        0
  MLPH WILD-TYPE        4        6        20        96         4        3
D104V3, multiclass
           clus
vv          MLPH MUTATED MLPH WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  MLPH MUTATED     0   1     2
  MLPH WILD-TYPE   5  12   116
D104V4, multiclass
       clus
vv      MLPH MUTATED MLPH WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            2            116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V5, binary
                cls
clus               0   1
  MLPH MUTATED     0   3
  MLPH WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      0    3
  MLPH WILD-TYPE   32  101
   clus
vv  MLPH MUTATED MLPH WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D104V6, binary
                cls
clus              0  1
  MLPH MUTATED    1  0
  MLPH WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      1    0
  MLPH WILD-TYPE   61    3
   clus
vv  MLPH MUTATED MLPH WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus              0  1
  MLPH MUTATED    2  1
  MLPH WILD-TYPE 60 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      2    1
  MLPH WILD-TYPE   60   73
        clus
vv       MLPH MUTATED MLPH WILD-TYPE
  FEMALE            2             60
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MLPH MUTATED                                     3
  MLPH WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MLPH MUTATED                                       0
  MLPH WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MLPH MUTATED                                                  0
  MLPH WILD-TYPE                                                2
D104V8, multiclass
                                                  clus
vv                                                 MLPH MUTATED MLPH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V9, continuous
D104V10, continuous
                vv
clus             R0 R1 R2 RX
  MLPH MUTATED    2  0  0  0
  MLPH WILD-TYPE 75 48  1  3
D104V11, multiclass
[1] "Remove cluster labels:" "MLPH MUTATED"          
clus
  MLPH MUTATED MLPH WILD-TYPE 
             2            127 
    TCGA-2J-AAB1     TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-2J-AAB9     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-2J-AABH     TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABR 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-2J-AABU     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-2L-AAQI     TCGA-2L-AAQJ     TCGA-2L-AAQL     TCGA-3A-A9I5 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-3A-A9I7     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IC 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-3A-A9IH     TCGA-3A-A9IU     TCGA-3A-A9IX     TCGA-3A-A9IZ 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-3A-A9J0     TCGA-F2-6879     TCGA-F2-A44G     TCGA-F2-A44H 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-F2-A7TX     TCGA-F2-A8YN     TCGA-FB-A4P5     TCGA-FB-A5VM 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPU     TCGA-FB-AAPY     TCGA-FB-AAPZ 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-FB-AAQ0     TCGA-FB-AAQ1     TCGA-FB-AAQ2     TCGA-FB-AAQ3 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-7919     TCGA-HZ-7922     TCGA-HZ-7925 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HZ-7926     TCGA-HZ-8001     TCGA-HZ-8002     TCGA-HZ-8003 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HZ-8005     TCGA-HZ-8315     TCGA-HZ-8317     TCGA-HZ-8519 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HZ-8636     TCGA-HZ-8637     TCGA-HZ-A49G     TCGA-HZ-A49H 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HZ-A49I     TCGA-HZ-A4BH     TCGA-HZ-A4BK     TCGA-HZ-A77O 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HZ-A77P     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7645     TCGA-IB-7646     TCGA-IB-7647 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7652     TCGA-IB-7885     TCGA-IB-7886 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7887     TCGA-IB-7888     TCGA-IB-7889     TCGA-IB-7890 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-7893     TCGA-IB-7897     TCGA-IB-8126 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-8127     TCGA-IB-A5SO     TCGA-IB-A5SP     TCGA-IB-A5SQ 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A5ST     TCGA-IB-A6UF     TCGA-IB-A6UG 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-A7LX     TCGA-IB-A7M4     TCGA-IB-AAUM     TCGA-IB-AAUN 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-AAUO     TCGA-IB-AAUP     TCGA-IB-AAUQ     TCGA-IB-AAUR 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-LB-A8F3     TCGA-LB-A9Q5     TCGA-M8-A5N4     TCGA-OE-A75W 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-Q3-A5QY     TCGA-Q3-AA2A     TCGA-RB-A7B8     TCGA-RB-AA9M 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-S4-A8RO     TCGA-S4-A8RP     TCGA-US-A774 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-US-A776     TCGA-US-A779     TCGA-US-A77E     TCGA-US-A77G 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-XD-AAUG     TCGA-XD-AAUH     TCGA-XD-AAUI     TCGA-XD-AAUL 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-YB-A89D     TCGA-YY-A8LH     TCGA-Z5-AAPL 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
D104V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLPH MUTATED       0                         0     3
  MLPH WILD-TYPE     2                         5   122
D104V13, multiclass
                           clus
vv                          MLPH MUTATED MLPH WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V14, binary
                cls
clus               0   1
  MLPH MUTATED     0   3
  MLPH WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      0    3
  MLPH WILD-TYPE    3  101
                        clus
vv                       MLPH MUTATED MLPH WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(105) Variable = UBXN4 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2              0  1
  UBXN4 MUTATED    0  3
  UBXN4 WILD-TYPE 62 69
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             131 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3              69 
$`UBXN4 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7887 
       20.19        19.82         3.62 

$`UBXN4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  UBXN4 MUTATED UBXN4 WILD-TYPE 
           3.62            0.13 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
          20.19           75.12 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
          19.82           13.68 
[1] "3.6 - 20.2 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2"  
D105V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UBXN4 MUTATED          0        0         0         3         0        0
  UBXN4 WILD-TYPE        4        6        20        96         4        3
D105V3, multiclass
           clus
vv          UBXN4 MUTATED UBXN4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  UBXN4 MUTATED     0   0     3
  UBXN4 WILD-TYPE   5  13   115
D105V4, multiclass
       clus
vv      UBXN4 MUTATED UBXN4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V5, binary
                 cls
clus                0   1
  UBXN4 MUTATED     0   3
  UBXN4 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      0    3
  UBXN4 WILD-TYPE   32  101
   clus
vv  UBXN4 MUTATED UBXN4 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D105V6, binary
                 cls
clus               0  1
  UBXN4 MUTATED    2  0
  UBXN4 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      2    0
  UBXN4 WILD-TYPE   60    3
   clus
vv  UBXN4 MUTATED UBXN4 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D105V7, binary
                 cls
clus               0  1
  UBXN4 MUTATED    2  1
  UBXN4 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      2    1
  UBXN4 WILD-TYPE   60   73
        clus
vv       UBXN4 MUTATED UBXN4 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBXN4 MUTATED                                     3
  UBXN4 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBXN4 MUTATED                                       0
  UBXN4 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBXN4 MUTATED                                                  0
  UBXN4 WILD-TYPE                                                2
D105V8, multiclass
                                                  clus
vv                                                 UBXN4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 UBXN4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V9, continuous
[1] "Remove cluster labels:" "UBXN4 MUTATED"         
clus
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
D105V10, continuous
[1] "Remove cluster labels:" "UBXN4 MUTATED"         
clus
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  UBXN4 MUTATED    2  1  0  0
  UBXN4 WILD-TYPE 75 47  1  3
D105V11, multiclass
    clus
vv   UBXN4 MUTATED UBXN4 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBXN4 MUTATED       0                         0     3
  UBXN4 WILD-TYPE     2                         5   122
D105V13, multiclass
                           clus
vv                          UBXN4 MUTATED UBXN4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V14, binary
                 cls
clus                0   1
  UBXN4 MUTATED     0   3
  UBXN4 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      0    3
  UBXN4 WILD-TYPE    3  101
                        clus
vv                       UBXN4 MUTATED UBXN4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(106) Variable = KCNE1 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2              0  1
  KCNE1 MUTATED    1  3
  KCNE1 WILD-TYPE 61 69
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             130 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              3              69 
$`KCNE1 MUTATED`
TCGA-F2-6879 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       10.98        20.19        19.82        41.33 

$`KCNE1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  KCNE1 MUTATED KCNE1 WILD-TYPE 
          10.98            0.13 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
          41.33           75.12 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
         20.005          13.500 
[1] "11.0 - 41.3 (20.0)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.1"
D106V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KCNE1 MUTATED          0        0         0         4         0        0
  KCNE1 WILD-TYPE        4        6        20        95         4        3
D106V3, multiclass
           clus
vv          KCNE1 MUTATED KCNE1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KCNE1 MUTATED     0   0     4
  KCNE1 WILD-TYPE   5  13   114
D106V4, multiclass
       clus
vv      KCNE1 MUTATED KCNE1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V5, binary
                 cls
clus                0   1
  KCNE1 MUTATED     0   4
  KCNE1 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      0    4
  KCNE1 WILD-TYPE   32  100
   clus
vv  KCNE1 MUTATED KCNE1 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D106V6, binary
                 cls
clus               0  1
  KCNE1 MUTATED    3  0
  KCNE1 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      3    0
  KCNE1 WILD-TYPE   59    3
   clus
vv  KCNE1 MUTATED KCNE1 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus               0  1
  KCNE1 MUTATED    2  2
  KCNE1 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      2    2
  KCNE1 WILD-TYPE   60   72
        clus
vv       KCNE1 MUTATED KCNE1 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNE1 MUTATED                                     3
  KCNE1 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNE1 MUTATED                                       1
  KCNE1 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNE1 MUTATED                                                  0
  KCNE1 WILD-TYPE                                                2
D106V8, multiclass
                                                  clus
vv                                                 KCNE1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KCNE1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V9, continuous
[1] "Remove cluster labels:" "KCNE1 MUTATED"         
clus
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
D106V10, continuous
[1] "Remove cluster labels:" "KCNE1 MUTATED"         
clus
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7891 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-YY-A8LH 
"KCNE1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KCNE1 MUTATED    4  0  0  0
  KCNE1 WILD-TYPE 73 48  1  3
D106V11, multiclass
    clus
vv   KCNE1 MUTATED KCNE1 WILD-TYPE
  R0             4              73
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNE1 MUTATED       0                         0     4
  KCNE1 WILD-TYPE     2                         5   121
D106V13, multiclass
                           clus
vv                          KCNE1 MUTATED KCNE1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V14, binary
                 cls
clus                0   1
  KCNE1 MUTATED     0   3
  KCNE1 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      0    3
  KCNE1 WILD-TYPE    3  101
                        clus
vv                       KCNE1 MUTATED KCNE1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(107) Variable = RTTN MUTATION ANALYSIS
D107V1, survival
                sevent
clus2             0  1
  RTTN MUTATED    1  4
  RTTN WILD-TYPE 61 68
  RTTN MUTATED RTTN WILD-TYPE 
             5            129 
  RTTN MUTATED RTTN WILD-TYPE 
             4             68 
$`RTTN MUTATED`
TCGA-HZ-7925 TCGA-HZ-A77Q TCGA-IB-7651 TCGA-US-A779 TCGA-US-A77E 
       20.19         1.08        19.82        16.80        14.14 

$`RTTN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
       21.60         5.26        10.85         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  RTTN MUTATED RTTN WILD-TYPE 
          1.08           0.13 
  RTTN MUTATED RTTN WILD-TYPE 
         20.19          75.12 
  RTTN MUTATED RTTN WILD-TYPE 
         16.80          13.32 
[1] "1.1 - 20.2 (16.8)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.6"
D107V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RTTN MUTATED          0        0         0         5         0        0
  RTTN WILD-TYPE        4        6        20        94         4        3
D107V3, multiclass
           clus
vv          RTTN MUTATED RTTN WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  RTTN MUTATED     0   0     5
  RTTN WILD-TYPE   5  13   113
D107V4, multiclass
       clus
vv      RTTN MUTATED RTTN WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V5, binary
                cls
clus              0  1
  RTTN MUTATED    0  5
  RTTN WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      0    5
  RTTN WILD-TYPE   32   99
   clus
vv  RTTN MUTATED RTTN WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D107V6, binary
                cls
clus              0  1
  RTTN MUTATED    1  0
  RTTN WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      1    0
  RTTN WILD-TYPE   61    3
   clus
vv  RTTN MUTATED RTTN WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D107V7, binary
                cls
clus              0  1
  RTTN MUTATED    3  2
  RTTN WILD-TYPE 59 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      3    2
  RTTN WILD-TYPE   59   72
        clus
vv       RTTN MUTATED RTTN WILD-TYPE
  FEMALE            3             59
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RTTN MUTATED                                     3
  RTTN WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RTTN MUTATED                                       2
  RTTN WILD-TYPE                                     9
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RTTN MUTATED                                                  0
  RTTN WILD-TYPE                                                2
D107V8, multiclass
                                                  clus
vv                                                 RTTN MUTATED RTTN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V9, continuous
[1] "Remove cluster labels:" "RTTN MUTATED"          
clus
  RTTN MUTATED RTTN WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7891 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" 
D107V10, continuous
[1] "Remove cluster labels:" "RTTN MUTATED"          
clus
  RTTN MUTATED RTTN WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-YY-A8LH 
"RTTN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RTTN MUTATED    4  1  0  0
  RTTN WILD-TYPE 73 47  1  3
D107V11, multiclass
    clus
vv   RTTN MUTATED RTTN WILD-TYPE
  R0            4             73
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RTTN MUTATED       0                         0     5
  RTTN WILD-TYPE     2                         5   120
D107V13, multiclass
                           clus
vv                          RTTN MUTATED RTTN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V14, binary
                cls
clus              0  1
  RTTN MUTATED    0  5
  RTTN WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      0    5
  RTTN WILD-TYPE    3   99
                        clus
vv                       RTTN MUTATED RTTN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             99
[1] 2 2
[1] FALSE

Clustering(108) Variable = FAM8A1 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2               0  1
  FAM8A1 MUTATED    3  1
  FAM8A1 WILD-TYPE 59 71
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              130 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               1               71 
$`FAM8A1 MUTATED`
TCGA-2J-AABK TCGA-3A-A9IX TCGA-IB-7644 TCGA-M8-A5N4 
       15.91        34.09        12.95        19.20 

$`FAM8A1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.22        22.72        22.26        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       15.06        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08         0.23        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           12.95             0.13 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           34.09            75.12 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
          17.555           13.500 
[1] "12.9 - 34.1 (17.6)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "3"  
D108V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FAM8A1 MUTATED          1        0         1         1         0        1
  FAM8A1 WILD-TYPE        3        6        19        98         4        2
D108V3, multiclass
           clus
vv          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              1               98
  STAGE III              0                4
  STAGE IV               1                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  FAM8A1 MUTATED     1   0     3
  FAM8A1 WILD-TYPE   4  13   115
D108V4, multiclass
       clus
vv      FAM8A1 MUTATED FAM8A1 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V5, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     2   2
  FAM8A1 WILD-TYPE  30 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    2
  FAM8A1 WILD-TYPE   30  102
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              2               30
  1              2              102
[1] 2 2
[1] FALSE
D108V6, binary
                  cls
clus                0  1
  FAM8A1 MUTATED    2  1
  FAM8A1 WILD-TYPE 60  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    1
  FAM8A1 WILD-TYPE   60    2
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              2               60
  1              1                2
[1] 2 2
[1] FALSE
D108V7, binary
                  cls
clus                0  1
  FAM8A1 MUTATED    2  2
  FAM8A1 WILD-TYPE 60 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    2
  FAM8A1 WILD-TYPE   60   72
        clus
vv       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  FEMALE              2               60
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM8A1 MUTATED                                     4
  FAM8A1 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM8A1 MUTATED                                       0
  FAM8A1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM8A1 MUTATED                                                  0
  FAM8A1 WILD-TYPE                                                2
D108V8, multiclass
                                                  clus
vv                                                 FAM8A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 FAM8A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V9, continuous
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-F2-A8YN       TCGA-FB-A4P5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7649       TCGA-IB-7651 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
D108V10, continuous
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7649 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YY-A8LH 
"FAM8A1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  FAM8A1 MUTATED    1  3  0  0
  FAM8A1 WILD-TYPE 76 45  1  3
D108V11, multiclass
    clus
vv   FAM8A1 MUTATED FAM8A1 WILD-TYPE
  R0              1               76
  R1              3               45
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM8A1 MUTATED       0                         0     3
  FAM8A1 WILD-TYPE     2                         5   122
D108V13, multiclass
                           clus
vv                          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V14, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     0   2
  FAM8A1 WILD-TYPE   3 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      0    2
  FAM8A1 WILD-TYPE    3  102
                        clus
vv                       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(109) Variable = ACTRT2 MUTATION ANALYSIS
D109V1, survival
                  sevent
clus2               0  1
  ACTRT2 MUTATED    1  2
  ACTRT2 WILD-TYPE 61 70
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              131 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               2               70 
$`ACTRT2 MUTATED`
TCGA-HZ-7925 TCGA-HZ-8519 TCGA-IB-7886 
       20.19        14.93         4.04 

$`ACTRT2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50         0.13        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
            4.04             0.13 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
           20.19            75.12 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
           14.93            13.68 
[1] "4.0 - 20.2 (14.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.6"
D109V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ACTRT2 MUTATED          1        0         0         2         0        0
  ACTRT2 WILD-TYPE        3        6        20        97         4        3
D109V3, multiclass
           clus
vv          ACTRT2 MUTATED ACTRT2 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ACTRT2 MUTATED     1   0     2
  ACTRT2 WILD-TYPE   4  13   116
D109V4, multiclass
       clus
vv      ACTRT2 MUTATED ACTRT2 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              2              116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V5, binary
                  cls
clus                 0   1
  ACTRT2 MUTATED     1   2
  ACTRT2 WILD-TYPE  31 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      1    2
  ACTRT2 WILD-TYPE   31  102
   clus
vv  ACTRT2 MUTATED ACTRT2 WILD-TYPE
  0              1               31
  1              2              102
[1] 2 2
[1] FALSE
D109V6, binary
                  cls
clus                0  1
  ACTRT2 MUTATED    1  0
  ACTRT2 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      1    0
  ACTRT2 WILD-TYPE   61    3
   clus
vv  ACTRT2 MUTATED ACTRT2 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D109V7, binary
                  cls
clus                0  1
  ACTRT2 MUTATED    0  3
  ACTRT2 WILD-TYPE 62 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      0    3
  ACTRT2 WILD-TYPE   62   71
        clus
vv       ACTRT2 MUTATED ACTRT2 WILD-TYPE
  FEMALE              0               62
  MALE                3               71
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACTRT2 MUTATED                                     2
  ACTRT2 WILD-TYPE                                 120
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACTRT2 MUTATED                                       1
  ACTRT2 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACTRT2 MUTATED                                                  0
  ACTRT2 WILD-TYPE                                                2
D109V8, multiclass
                                                  clus
vv                                                 ACTRT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ACTRT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V9, continuous
[1] "Remove cluster labels:" "ACTRT2 MUTATED"        
clus
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7887 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
D109V10, continuous
[1] "Remove cluster labels:" "ACTRT2 MUTATED"        
clus
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ACTRT2 MUTATED    2  1  0  0
  ACTRT2 WILD-TYPE 75 47  1  3
D109V11, multiclass
    clus
vv   ACTRT2 MUTATED ACTRT2 WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACTRT2 MUTATED       0                         0     3
  ACTRT2 WILD-TYPE     2                         5   122
D109V13, multiclass
                           clus
vv                          ACTRT2 MUTATED ACTRT2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V14, binary
                  cls
clus                 0   1
  ACTRT2 MUTATED     0   3
  ACTRT2 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      0    3
  ACTRT2 WILD-TYPE    3  101
                        clus
vv                       ACTRT2 MUTATED ACTRT2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(110) Variable = DNAH7 MUTATION ANALYSIS
D110V1, survival
                 sevent
clus2              0  1
  DNAH7 MUTATED    4  3
  DNAH7 WILD-TYPE 58 69
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             127 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              3              69 
$`DNAH7 MUTATED`
TCGA-FB-AAPZ TCGA-HZ-7925 TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7885 TCGA-PZ-A5RE 
       23.54        20.19         1.08        19.82        41.33        15.45 
TCGA-RB-AA9M 
        9.40 

$`DNAH7 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        15.35        23.80         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       13.68         3.12        15.32        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  DNAH7 MUTATED DNAH7 WILD-TYPE 
           1.08            0.13 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          41.33           75.12 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          19.82           13.32 
[1] "1.1 - 41.3 (19.8)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.6"
D110V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DNAH7 MUTATED          0        0         0         7         0        0
  DNAH7 WILD-TYPE        4        6        20        92         4        3
D110V3, multiclass
           clus
vv          DNAH7 MUTATED DNAH7 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             7              92
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  DNAH7 MUTATED     1   1     5
  DNAH7 WILD-TYPE   4  12   113
D110V4, multiclass
       clus
vv      DNAH7 MUTATED DNAH7 WILD-TYPE
  T1                1               4
  T2                1              12
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V5, binary
                 cls
clus               0  1
  DNAH7 MUTATED    0  7
  DNAH7 WILD-TYPE 32 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    7
  DNAH7 WILD-TYPE   32   97
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             0              32
  1             7              97
[1] 2 2
[1] FALSE
D110V6, binary
                 cls
clus               0  1
  DNAH7 MUTATED    2  0
  DNAH7 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      2    0
  DNAH7 WILD-TYPE   60    3
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D110V7, binary
                 cls
clus               0  1
  DNAH7 MUTATED    4  3
  DNAH7 WILD-TYPE 58 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      4    3
  DNAH7 WILD-TYPE   58   71
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE             4              58
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DNAH7 MUTATED                                     6
  DNAH7 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DNAH7 MUTATED                                       1
  DNAH7 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DNAH7 MUTATED                                                  0
  DNAH7 WILD-TYPE                                                2
D110V8, multiclass
                                                  clus
vv                                                 DNAH7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DNAH7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V9, continuous
D110V10, continuous
                 vv
clus              R0 R1 R2 RX
  DNAH7 MUTATED    6  0  0  0
  DNAH7 WILD-TYPE 71 48  1  3
D110V11, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  R0             6              71
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH7 MUTATED       0                         0     7
  DNAH7 WILD-TYPE     2                         5   118
D110V13, multiclass
                           clus
vv                          DNAH7 MUTATED DNAH7 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V14, binary
                 cls
clus               0  1
  DNAH7 MUTATED    0  7
  DNAH7 WILD-TYPE  3 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    7
  DNAH7 WILD-TYPE    3   97
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7              97
[1] 2 2
[1] FALSE

Clustering(111) Variable = OR1N2 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2              0  1
  OR1N2 MUTATED    0  4
  OR1N2 WILD-TYPE 62 68
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              4             130 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              4              68 
$`OR1N2 MUTATED`
TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-AAUO 
       71.74        19.82        43.79         7.86 

$`OR1N2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04         3.62        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  OR1N2 MUTATED OR1N2 WILD-TYPE 
           7.86            0.13 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
          71.74           75.12 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
         31.805          13.500 
[1] "7.9 - 71.7 (31.8)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.2"
D111V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR1N2 MUTATED          0        0         2         2         0        0
  OR1N2 WILD-TYPE        4        6        18        97         4        3
D111V3, multiclass
           clus
vv          OR1N2 MUTATED OR1N2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  OR1N2 MUTATED     0   0     4
  OR1N2 WILD-TYPE   5  13   114
D111V4, multiclass
       clus
vv      OR1N2 MUTATED OR1N2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V5, binary
                 cls
clus                0   1
  OR1N2 MUTATED     2   2
  OR1N2 WILD-TYPE  30 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      2    2
  OR1N2 WILD-TYPE   30  102
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             2              30
  1             2             102
[1] 2 2
[1] FALSE
D111V6, binary
                 cls
clus               0  1
  OR1N2 MUTATED    3  0
  OR1N2 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      3    0
  OR1N2 WILD-TYPE   59    3
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D111V7, binary
                 cls
clus               0  1
  OR1N2 MUTATED    3  1
  OR1N2 WILD-TYPE 59 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      3    1
  OR1N2 WILD-TYPE   59   73
        clus
vv       OR1N2 MUTATED OR1N2 WILD-TYPE
  FEMALE             3              59
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR1N2 MUTATED                                     4
  OR1N2 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR1N2 MUTATED                                       0
  OR1N2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR1N2 MUTATED                                                  0
  OR1N2 WILD-TYPE                                                2
D111V8, multiclass
                                                  clus
vv                                                 OR1N2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 OR1N2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V9, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
D111V10, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR1N2 MUTATED    2  1  0  0
  OR1N2 WILD-TYPE 75 47  1  3
D111V11, multiclass
    clus
vv   OR1N2 MUTATED OR1N2 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR1N2 MUTATED       0                         1     3
  OR1N2 WILD-TYPE     2                         4   122
D111V13, multiclass
                           clus
vv                          OR1N2 MUTATED OR1N2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V14, binary
                 cls
clus                0   1
  OR1N2 MUTATED     1   3
  OR1N2 WILD-TYPE   2 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      1    3
  OR1N2 WILD-TYPE    2  101
                        clus
vv                       OR1N2 MUTATED OR1N2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(112) Variable = BRD8 MUTATION ANALYSIS
D112V1, survival
                sevent
clus2             0  1
  BRD8 MUTATED    0  3
  BRD8 WILD-TYPE 62 69
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            131 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3             69 
$`BRD8 MUTATED`
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-IB-7651 
       20.19        17.03        19.82 

$`BRD8 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 
        1.02        12.89        13.84        19.50         0.13        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  BRD8 MUTATED BRD8 WILD-TYPE 
         17.03           0.13 
  BRD8 MUTATED BRD8 WILD-TYPE 
         20.19          75.12 
  BRD8 MUTATED BRD8 WILD-TYPE 
         19.82          13.32 
[1] "17.0 - 20.2 (19.8)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.4"
D112V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BRD8 MUTATED          0        0         0         3         0        0
  BRD8 WILD-TYPE        4        6        20        96         4        3
D112V3, multiclass
           clus
vv          BRD8 MUTATED BRD8 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  BRD8 MUTATED     0   0     3
  BRD8 WILD-TYPE   5  13   115
D112V4, multiclass
       clus
vv      BRD8 MUTATED BRD8 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V5, binary
                cls
clus               0   1
  BRD8 MUTATED     0   3
  BRD8 WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      0    3
  BRD8 WILD-TYPE   32  101
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D112V6, binary
                cls
clus              0  1
  BRD8 MUTATED    1  0
  BRD8 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      1    0
  BRD8 WILD-TYPE   61    3
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus              0  1
  BRD8 MUTATED    1  2
  BRD8 WILD-TYPE 61 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      1    2
  BRD8 WILD-TYPE   61   72
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE            1             61
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRD8 MUTATED                                     3
  BRD8 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRD8 MUTATED                                       0
  BRD8 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRD8 MUTATED                                                  0
  BRD8 WILD-TYPE                                                2
D112V8, multiclass
                                                  clus
vv                                                 BRD8 MUTATED BRD8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V9, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
D112V10, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BRD8 MUTATED    2  0  0  1
  BRD8 WILD-TYPE 75 48  1  2
D112V11, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0            2             75
  R1            0             48
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRD8 MUTATED       0                         1     2
  BRD8 WILD-TYPE     2                         4   123
D112V13, multiclass
                           clus
vv                          BRD8 MUTATED BRD8 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                2            123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V14, binary
                cls
clus               0   1
  BRD8 MUTATED     0   3
  BRD8 WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      0    3
  BRD8 WILD-TYPE    3  101
                        clus
vv                       BRD8 MUTATED BRD8 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(113) Variable = MIPEP MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2              0  1
  MIPEP MUTATED    0  3
  MIPEP WILD-TYPE 62 69
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             131 
  MIPEP MUTATED MIPEP WILD-TYPE 
              3              69 
$`MIPEP MUTATED`
TCGA-F2-6879 TCGA-HZ-8005 TCGA-IB-7887 
       10.98         3.95         3.62 

$`MIPEP WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  MIPEP MUTATED MIPEP WILD-TYPE 
           3.62            0.13 
  MIPEP MUTATED MIPEP WILD-TYPE 
          10.98           75.12 
  MIPEP MUTATED MIPEP WILD-TYPE 
           3.95           13.84 
[1] "3.6 - 11.0 (4.0)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "7.7"
D113V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MIPEP MUTATED          0        0         0         3         0        0
  MIPEP WILD-TYPE        4        6        20        96         4        3
D113V3, multiclass
           clus
vv          MIPEP MUTATED MIPEP WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  MIPEP MUTATED     0   0     3
  MIPEP WILD-TYPE   5  13   115
D113V4, multiclass
       clus
vv      MIPEP MUTATED MIPEP WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V5, binary
                 cls
clus                0   1
  MIPEP MUTATED     0   3
  MIPEP WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      0    3
  MIPEP WILD-TYPE   32  101
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D113V6, binary
                 cls
clus               0  1
  MIPEP MUTATED    2  0
  MIPEP WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      2    0
  MIPEP WILD-TYPE   60    3
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus               0  1
  MIPEP MUTATED    1  2
  MIPEP WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      1    2
  MIPEP WILD-TYPE   61   72
        clus
vv       MIPEP MUTATED MIPEP WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MIPEP MUTATED                                     2
  MIPEP WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MIPEP MUTATED                                       1
  MIPEP WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MIPEP MUTATED                                                  0
  MIPEP WILD-TYPE                                                2
D113V8, multiclass
                                                  clus
vv                                                 MIPEP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 MIPEP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V9, continuous
[1] "Remove cluster labels:" "MIPEP MUTATED"         
clus
  MIPEP MUTATED MIPEP WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
D113V10, continuous
                 vv
clus              R0 R1 R2 RX
  MIPEP MUTATED    1  2  0  0
  MIPEP WILD-TYPE 76 46  1  3
D113V11, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MIPEP MUTATED       0                         0     3
  MIPEP WILD-TYPE     2                         5   122
D113V13, multiclass
                           clus
vv                          MIPEP MUTATED MIPEP WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V14, binary
                 cls
clus                0   1
  MIPEP MUTATED     0   2
  MIPEP WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      0    2
  MIPEP WILD-TYPE    3  102
                        clus
vv                       MIPEP MUTATED MIPEP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(114) Variable = SIGLEC14 MUTATION ANALYSIS
D114V1, survival
                    sevent
clus2                 0  1
  SIGLEC14 MUTATED    0  3
  SIGLEC14 WILD-TYPE 62 69
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                131 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                 69 
$`SIGLEC14 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-HZ-8317 
        2.17         9.63        12.43 

$`SIGLEC14 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
       23.97         2.63        20.61        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.26        15.91        14.47        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         3.95         9.83        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              2.17               0.13 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             12.43              75.12 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              9.63              13.84 
[1] "2.2 - 12.4 (9.6)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "5.2"
D114V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SIGLEC14 MUTATED          0        0         1         2         0        0
  SIGLEC14 WILD-TYPE        4        6        19        97         4        3
D114V3, multiclass
           clus
vv          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE IA                 0                  4
  STAGE IB                 0                  6
  STAGE IIA                1                 19
  STAGE IIB                2                 97
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  SIGLEC14 MUTATED     0   0     3
  SIGLEC14 WILD-TYPE   5  13   115
D114V4, multiclass
       clus
vv      SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                   0                  5
  T2                   0                 13
  T3+T4                3                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V5, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     1   2
  SIGLEC14 WILD-TYPE  31 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      1    2
  SIGLEC14 WILD-TYPE   31  102
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                1                 31
  1                2                102
[1] 2 2
[1] FALSE
D114V6, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    2  0
  SIGLEC14 WILD-TYPE 60  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      2    0
  SIGLEC14 WILD-TYPE   60    3
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                2                 60
  1                0                  3
[1] 2 2
[1] FALSE
D114V7, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    1  2
  SIGLEC14 WILD-TYPE 61 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      1    2
  SIGLEC14 WILD-TYPE   61   72
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                1                 61
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIGLEC14 MUTATED                                     2
  SIGLEC14 WILD-TYPE                                 120
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIGLEC14 MUTATED                                       1
  SIGLEC14 WILD-TYPE                                    10
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIGLEC14 MUTATED                                                  0
  SIGLEC14 WILD-TYPE                                                2
D114V8, multiclass
                                                  clus
vv                                                 SIGLEC14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 SIGLEC14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V9, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 1                 47 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A4P5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-A4P6         TCGA-FB-A5VM         TCGA-FB-A78T 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPY         TCGA-H6-8124 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-H6-A45N         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
D114V10, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 1                 38 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-FB-A4P5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-A4P6         TCGA-FB-A5VM         TCGA-FB-A78T 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPY         TCGA-H6-8124 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7891 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-US-A774         TCGA-XD-AAUI 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  SIGLEC14 MUTATED    2  1  0  0
  SIGLEC14 WILD-TYPE 75 47  1  3
D114V11, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                2                 75
  R1                1                 47
  R2                0                  1
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC14 MUTATED       0                         0     3
  SIGLEC14 WILD-TYPE     2                         5   122
D114V13, multiclass
                           clus
vv                          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V14, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     0   1
  SIGLEC14 WILD-TYPE   3 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      0    1
  SIGLEC14 WILD-TYPE    3  103
                        clus
vv                       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                1                103
[1] 2 2
[1] FALSE

Clustering(115) Variable = ARID1A MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    4  3
  ARID1A WILD-TYPE 58 69
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              127 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               69 
$`ARID1A MUTATED`
TCGA-2J-AABA TCGA-F2-A7TX TCGA-HZ-8001 TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-AAUR 
       19.96         3.12        23.21         0.23        19.82        11.11 
TCGA-YY-A8LH 
       66.28 

$`ARID1A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       10.98         7.66        19.27        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 
       13.84        19.50         0.13        20.19        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         1.08        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
        7.86        14.17         6.02         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-Z5-AAPL 
        0.69 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.23             0.13 
  ARID1A MUTATED ARID1A WILD-TYPE 
           66.28            75.12 
  ARID1A MUTATED ARID1A WILD-TYPE 
           19.82            13.68 
[1] "0.2 - 66.3 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.6"
D115V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ARID1A MUTATED          0        1         0         5         1        0
  ARID1A WILD-TYPE        4        5        20        94         3        3
D115V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE IA               0                4
  STAGE IB               1                5
  STAGE IIA              0               20
  STAGE IIB              5               94
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ARID1A MUTATED     0   1     6
  ARID1A WILD-TYPE   5  12   112
D115V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              6              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  5
  ARID1A WILD-TYPE 30 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   30   99
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              2               30
  1              5               99
[1] 2 2
[1] FALSE
D115V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    4  0
  ARID1A WILD-TYPE 58  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    0
  ARID1A WILD-TYPE   58    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              4               58
  1              0                3
[1] 2 2
[1] FALSE
D115V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  5
  ARID1A WILD-TYPE 60 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   60   69
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              2               60
  MALE                5               69
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARID1A MUTATED                                     7
  ARID1A WILD-TYPE                                 115
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARID1A MUTATED                                       0
  ARID1A WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARID1A MUTATED                                                  0
  ARID1A WILD-TYPE                                                2
D115V8, multiclass
                                                  clus
vv                                                 ARID1A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ARID1A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V9, continuous
D115V10, continuous
                  vv
clus               R0 R1 R2 RX
  ARID1A MUTATED    4  3  0  0
  ARID1A WILD-TYPE 73 45  1  3
D115V11, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              4               73
  R1              3               45
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0     7
  ARID1A WILD-TYPE     2                         5   118
D115V13, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V14, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  5
  ARID1A WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    5
  ARID1A WILD-TYPE    3   99
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(116) Variable = POM121 MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2               0  1
  POM121 MUTATED    1  3
  POM121 WILD-TYPE 61 69
  POM121 MUTATED POM121 WILD-TYPE 
               4              130 
  POM121 MUTATED POM121 WILD-TYPE 
               3               69 
$`POM121 MUTATED`
TCGA-HZ-7922 TCGA-IB-7651 TCGA-IB-A5SQ TCGA-LB-A9Q5 
        0.13        19.82         7.20        10.29 

$`POM121 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 
        1.02        12.89        13.84        19.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        7.40         9.44         8.05        12.92        12.46        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  POM121 MUTATED POM121 WILD-TYPE 
            0.13             0.23 
  POM121 MUTATED POM121 WILD-TYPE 
           19.82            75.12 
  POM121 MUTATED POM121 WILD-TYPE 
           8.745           13.825 
[1] "0.1 - 19.8 (8.7)"  "0.2 - 75.1 (13.8)"
[1] "hr=" "2.6"
D116V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  POM121 MUTATED          0        1         0         3         0        0
  POM121 WILD-TYPE        4        5        20        96         4        3
D116V3, multiclass
           clus
vv          POM121 MUTATED POM121 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               1                5
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  POM121 MUTATED     0   1     3
  POM121 WILD-TYPE   5  12   115
D116V4, multiclass
       clus
vv      POM121 MUTATED POM121 WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V5, binary
                  cls
clus                 0   1
  POM121 MUTATED     1   3
  POM121 WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      1    3
  POM121 WILD-TYPE   31  101
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D116V6, binary
                  cls
clus                0  1
  POM121 MUTATED    2  0
  POM121 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    0
  POM121 WILD-TYPE   60    3
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D116V7, binary
                  cls
clus                0  1
  POM121 MUTATED    4  0
  POM121 WILD-TYPE 58 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      4    0
  POM121 WILD-TYPE   58   74
        clus
vv       POM121 MUTATED POM121 WILD-TYPE
  FEMALE              4               58
  MALE                0               74
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POM121 MUTATED                                     4
  POM121 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POM121 MUTATED                                       0
  POM121 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POM121 MUTATED                                                  0
  POM121 WILD-TYPE                                                2
D116V8, multiclass
                                                  clus
vv                                                 POM121 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 POM121 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V9, continuous
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" 
D116V10, continuous
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-OE-A75W 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-YY-A8LH 
"POM121 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  POM121 MUTATED    4  0  0  0
  POM121 WILD-TYPE 73 48  1  3
D116V11, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  R0              4               73
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POM121 MUTATED       0                         0     4
  POM121 WILD-TYPE     2                         5   121
D116V13, multiclass
                           clus
vv                          POM121 MUTATED POM121 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V14, binary
                  cls
clus                 0   1
  POM121 MUTATED     0   4
  POM121 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      0    4
  POM121 WILD-TYPE    3  100
                        clus
vv                       POM121 MUTATED POM121 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(117) Variable = LCP2 MUTATION ANALYSIS
D117V1, survival
                sevent
clus2             0  1
  LCP2 MUTATED    1  2
  LCP2 WILD-TYPE 61 70
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            131 
  LCP2 MUTATED LCP2 WILD-TYPE 
             2             70 
$`LCP2 MUTATED`
TCGA-3E-AAAY TCGA-HZ-7925 TCGA-IB-7651 
       75.12        20.19        19.82 

$`LCP2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       28.73        15.06        34.09        10.13        12.39        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  LCP2 MUTATED LCP2 WILD-TYPE 
         19.82           0.13 
  LCP2 MUTATED LCP2 WILD-TYPE 
         75.12          71.74 
  LCP2 MUTATED LCP2 WILD-TYPE 
         20.19          13.32 
[1] "19.8 - 75.1 (20.2)" "0.1 - 71.7 (13.3)" 
[1] "hr=" "2"  
D117V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LCP2 MUTATED          0        0         0         3         0        0
  LCP2 WILD-TYPE        4        6        20        96         4        3
D117V3, multiclass
           clus
vv          LCP2 MUTATED LCP2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  LCP2 MUTATED     0   0     3
  LCP2 WILD-TYPE   5  13   115
D117V4, multiclass
       clus
vv      LCP2 MUTATED LCP2 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V5, binary
                cls
clus               0   1
  LCP2 MUTATED     0   3
  LCP2 WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      0    3
  LCP2 WILD-TYPE   32  101
   clus
vv  LCP2 MUTATED LCP2 WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D117V6, binary
                cls
clus              0  1
  LCP2 MUTATED    1  0
  LCP2 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      1    0
  LCP2 WILD-TYPE   61    3
   clus
vv  LCP2 MUTATED LCP2 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D117V7, binary
                cls
clus              0  1
  LCP2 MUTATED    1  2
  LCP2 WILD-TYPE 61 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      1    2
  LCP2 WILD-TYPE   61   72
        clus
vv       LCP2 MUTATED LCP2 WILD-TYPE
  FEMALE            1             61
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LCP2 MUTATED                                     3
  LCP2 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LCP2 MUTATED                                       0
  LCP2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LCP2 MUTATED                                                  0
  LCP2 WILD-TYPE                                                2
D117V8, multiclass
                                                  clus
vv                                                 LCP2 MUTATED LCP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V9, continuous
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
D117V10, continuous
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  LCP2 MUTATED    2  0  0  0
  LCP2 WILD-TYPE 75 48  1  3
D117V11, multiclass
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             2            127 
    TCGA-2J-AAB1     TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-2J-AAB9     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-2J-AABH     TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABR 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-2J-AABU     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-2L-AAQI     TCGA-2L-AAQJ     TCGA-2L-AAQL     TCGA-3A-A9I5 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-3A-A9I7     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IC 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-3A-A9IH     TCGA-3A-A9IU     TCGA-3A-A9IX     TCGA-3A-A9IZ 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-3A-A9J0     TCGA-F2-6879     TCGA-F2-A44G     TCGA-F2-A44H 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-F2-A7TX     TCGA-F2-A8YN     TCGA-FB-A4P5     TCGA-FB-A5VM 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPU     TCGA-FB-AAPY 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-AAPZ     TCGA-FB-AAQ0     TCGA-FB-AAQ1     TCGA-FB-AAQ2 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-FB-AAQ3     TCGA-H6-8124     TCGA-HZ-7919     TCGA-HZ-7922 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-7926     TCGA-HZ-8001     TCGA-HZ-8002     TCGA-HZ-8003 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-8005     TCGA-HZ-8315     TCGA-HZ-8317     TCGA-HZ-8519 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-8636     TCGA-HZ-8637     TCGA-HZ-A49G     TCGA-HZ-A49H 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-A49I     TCGA-HZ-A4BH     TCGA-HZ-A4BK     TCGA-HZ-A77O 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HZ-A77P     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7645     TCGA-IB-7646     TCGA-IB-7647 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7652     TCGA-IB-7885     TCGA-IB-7886 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7887     TCGA-IB-7888     TCGA-IB-7889     TCGA-IB-7890 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-7893     TCGA-IB-7897     TCGA-IB-8126 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-8127     TCGA-IB-A5SO     TCGA-IB-A5SP     TCGA-IB-A5SQ 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A5ST     TCGA-IB-A6UF     TCGA-IB-A6UG 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A7LX     TCGA-IB-A7M4     TCGA-IB-AAUM     TCGA-IB-AAUN 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUO     TCGA-IB-AAUP     TCGA-IB-AAUQ     TCGA-IB-AAUR 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-LB-A8F3     TCGA-LB-A9Q5     TCGA-M8-A5N4     TCGA-OE-A75W 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-Q3-A5QY     TCGA-Q3-AA2A     TCGA-RB-A7B8     TCGA-RB-AA9M 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-S4-A8RO     TCGA-S4-A8RP     TCGA-US-A774 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-US-A776     TCGA-US-A779     TCGA-US-A77E     TCGA-US-A77G 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-XD-AAUG     TCGA-XD-AAUH     TCGA-XD-AAUI     TCGA-XD-AAUL 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-YB-A89D     TCGA-YY-A8LH     TCGA-Z5-AAPL 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
D117V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LCP2 MUTATED       0                         0     3
  LCP2 WILD-TYPE     2                         5   122
D117V13, multiclass
                           clus
vv                          LCP2 MUTATED LCP2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V14, binary
                cls
clus               0   1
  LCP2 MUTATED     0   3
  LCP2 WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      0    3
  LCP2 WILD-TYPE    3  101
                        clus
vv                       LCP2 MUTATED LCP2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(118) Variable = L1CAM MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2              0  1
  L1CAM MUTATED    0  5
  L1CAM WILD-TYPE 62 67
  L1CAM MUTATED L1CAM WILD-TYPE 
              5             129 
  L1CAM MUTATED L1CAM WILD-TYPE 
              5              67 
$`L1CAM MUTATED`
TCGA-2J-AAB9 TCGA-HZ-7925 TCGA-IB-AAUO TCGA-US-A774 TCGA-US-A77E 
       20.61        20.19         7.86        22.85        14.14 

$`L1CAM WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
        9.40        21.24        17.26        23.08        27.75        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  L1CAM MUTATED L1CAM WILD-TYPE 
           7.86            0.13 
  L1CAM MUTATED L1CAM WILD-TYPE 
          22.85           75.12 
  L1CAM MUTATED L1CAM WILD-TYPE 
          20.19           13.32 
[1] "7.9 - 22.9 (20.2)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.6"
D118V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  L1CAM MUTATED          0        0         0         5         0        0
  L1CAM WILD-TYPE        4        6        20        94         4        3
D118V3, multiclass
           clus
vv          L1CAM MUTATED L1CAM WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  L1CAM MUTATED     0   0     5
  L1CAM WILD-TYPE   5  13   113
D118V4, multiclass
       clus
vv      L1CAM MUTATED L1CAM WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V5, binary
                 cls
clus               0  1
  L1CAM MUTATED    0  5
  L1CAM WILD-TYPE 32 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      0    5
  L1CAM WILD-TYPE   32   99
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             0              32
  1             5              99
[1] 2 2
[1] FALSE
D118V6, binary
                 cls
clus               0  1
  L1CAM MUTATED    2  0
  L1CAM WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      2    0
  L1CAM WILD-TYPE   60    3
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus               0  1
  L1CAM MUTATED    3  2
  L1CAM WILD-TYPE 59 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      3    2
  L1CAM WILD-TYPE   59   72
        clus
vv       L1CAM MUTATED L1CAM WILD-TYPE
  FEMALE             3              59
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  L1CAM MUTATED                                     4
  L1CAM WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  L1CAM MUTATED                                       1
  L1CAM WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  L1CAM MUTATED                                                  0
  L1CAM WILD-TYPE                                                2
D118V8, multiclass
                                                  clus
vv                                                 L1CAM MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 L1CAM WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V9, continuous
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-XD-AAUL      TCGA-YY-A8LH 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
D118V10, continuous
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-XD-AAUI 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  L1CAM MUTATED    3  2  0  0
  L1CAM WILD-TYPE 74 46  1  3
D118V11, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  R0             3              74
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  L1CAM MUTATED       0                         0     5
  L1CAM WILD-TYPE     2                         5   120
D118V13, multiclass
                           clus
vv                          L1CAM MUTATED L1CAM WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V14, binary
                 cls
clus                0   1
  L1CAM MUTATED     0   4
  L1CAM WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      0    4
  L1CAM WILD-TYPE    3  100
                        clus
vv                       L1CAM MUTATED L1CAM WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(119) Variable = ABCG5 MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2              0  1
  ABCG5 MUTATED    0  3
  ABCG5 WILD-TYPE 62 69
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              3             131 
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              3              69 
$`ABCG5 MUTATED`
TCGA-HZ-8005 TCGA-IB-7644 TCGA-IB-7651 
        3.95        12.95        19.82 

$`ABCG5 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 
       21.60         5.26        10.85         1.08         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ABCG5 MUTATED ABCG5 WILD-TYPE 
           3.95            0.13 
  ABCG5 MUTATED ABCG5 WILD-TYPE 
          19.82           75.12 
  ABCG5 MUTATED ABCG5 WILD-TYPE 
          12.95           13.81 
[1] "4.0 - 19.8 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.6"
D119V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ABCG5 MUTATED          0        0         0         2         0        1
  ABCG5 WILD-TYPE        4        6        20        97         4        2
D119V3, multiclass
           clus
vv          ABCG5 MUTATED ABCG5 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ABCG5 MUTATED     0   0     3
  ABCG5 WILD-TYPE   5  13   115
D119V4, multiclass
       clus
vv      ABCG5 MUTATED ABCG5 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V5, binary
                 cls
clus                0   1
  ABCG5 MUTATED     0   3
  ABCG5 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG5 MUTATED      0    3
  ABCG5 WILD-TYPE   32  101
   clus
vv  ABCG5 MUTATED ABCG5 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D119V6, binary
                 cls
clus               0  1
  ABCG5 MUTATED    1  1
  ABCG5 WILD-TYPE 61  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG5 MUTATED      1    1
  ABCG5 WILD-TYPE   61    2
   clus
vv  ABCG5 MUTATED ABCG5 WILD-TYPE
  0             1              61
  1             1               2
[1] 2 2
[1] FALSE
D119V7, binary
                 cls
clus               0  1
  ABCG5 MUTATED    2  1
  ABCG5 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG5 MUTATED      2    1
  ABCG5 WILD-TYPE   60   73
        clus
vv       ABCG5 MUTATED ABCG5 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ABCG5 MUTATED                                     3
  ABCG5 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ABCG5 MUTATED                                       0
  ABCG5 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ABCG5 MUTATED                                                  0
  ABCG5 WILD-TYPE                                                2
D119V8, multiclass
                                                  clus
vv                                                 ABCG5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ABCG5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V9, continuous
[1] "Remove cluster labels:" "ABCG5 MUTATED"         
clus
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7649 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
D119V10, continuous
[1] "Remove cluster labels:" "ABCG5 MUTATED"         
clus
  ABCG5 MUTATED ABCG5 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" "ABCG5 WILD-TYPE" 
     TCGA-YY-A8LH 
"ABCG5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ABCG5 MUTATED    1  2  0  0
  ABCG5 WILD-TYPE 76 46  1  3
D119V11, multiclass
    clus
vv   ABCG5 MUTATED ABCG5 WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCG5 MUTATED       0                         0     3
  ABCG5 WILD-TYPE     2                         5   122
D119V13, multiclass
                           clus
vv                          ABCG5 MUTATED ABCG5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V14, binary
                 cls
clus                0   1
  ABCG5 MUTATED     0   3
  ABCG5 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG5 MUTATED      0    3
  ABCG5 WILD-TYPE    3  101
                        clus
vv                       ABCG5 MUTATED ABCG5 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(120) Variable = KRT2 MUTATION ANALYSIS
D120V1, survival
                sevent
clus2             0  1
  KRT2 MUTATED    2  3
  KRT2 WILD-TYPE 60 69
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            129 
  KRT2 MUTATED KRT2 WILD-TYPE 
             3             69 
$`KRT2 MUTATED`
TCGA-FB-AAPY TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-HZ-8003 TCGA-IB-7651 
       34.82         1.02        12.89         0.69        19.82 

$`KRT2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-A45N 
       12.53        23.54        15.55         4.04         5.03        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  KRT2 MUTATED KRT2 WILD-TYPE 
          0.69           0.13 
  KRT2 MUTATED KRT2 WILD-TYPE 
         34.82          75.12 
  KRT2 MUTATED KRT2 WILD-TYPE 
         12.89          13.81 
[1] "0.7 - 34.8 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.2"
D120V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KRT2 MUTATED          0        0         0         5         0        0
  KRT2 WILD-TYPE        4        6        20        94         4        3
D120V3, multiclass
           clus
vv          KRT2 MUTATED KRT2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  KRT2 MUTATED     0   1     4
  KRT2 WILD-TYPE   5  12   114
D120V4, multiclass
       clus
vv      KRT2 MUTATED KRT2 WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V5, binary
                cls
clus              0  1
  KRT2 MUTATED    0  5
  KRT2 WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0    5
  KRT2 WILD-TYPE   32   99
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D120V6, binary
                cls
clus              0  1
  KRT2 MUTATED    2  0
  KRT2 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      2    0
  KRT2 WILD-TYPE   60    3
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D120V7, binary
                cls
clus              0  1
  KRT2 MUTATED    4  1
  KRT2 WILD-TYPE 58 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      4    1
  KRT2 WILD-TYPE   58   73
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            4             58
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRT2 MUTATED                                     5
  KRT2 WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRT2 MUTATED                                       0
  KRT2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRT2 MUTATED                                                  0
  KRT2 WILD-TYPE                                                2
D120V8, multiclass
                                                  clus
vv                                                 KRT2 MUTATED KRT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V9, continuous
D120V10, continuous
                vv
clus             R0 R1 R2 RX
  KRT2 MUTATED    5  0  0  0
  KRT2 WILD-TYPE 72 48  1  3
D120V11, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0            5             72
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED       0                         0     5
  KRT2 WILD-TYPE     2                         5   120
D120V13, multiclass
                           clus
vv                          KRT2 MUTATED KRT2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V14, binary
                cls
clus              0  1
  KRT2 MUTATED    0  5
  KRT2 WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0    5
  KRT2 WILD-TYPE    3   99
                        clus
vv                       KRT2 MUTATED KRT2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             99
[1] 2 2
[1] FALSE

Clustering(121) Variable = ZNF780A MUTATION ANALYSIS
D121V1, survival
                   sevent
clus2                0  1
  ZNF780A MUTATED    2  3
  ZNF780A WILD-TYPE 60 69
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               129 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                3                69 
$`ZNF780A MUTATED`
TCGA-HZ-A8P1 TCGA-IB-8126 TCGA-IB-A5SS TCGA-US-A779 TCGA-US-A77E 
        0.23         2.47        15.12        16.80        14.14 

$`ZNF780A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
        6.38        21.60         5.26        10.85         1.08        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
       21.30         3.85        15.98        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  ZNF780A MUTATED ZNF780A WILD-TYPE 
             0.23              0.13 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            16.80             75.12 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            14.14             13.68 
[1] "0.2 - 16.8 (14.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2"  
D121V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF780A MUTATED          0        1         0         3         1        0
  ZNF780A WILD-TYPE        4        5        20        96         3        3
D121V3, multiclass
           clus
vv          ZNF780A MUTATED ZNF780A WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                1                 5
  STAGE IIA               0                20
  STAGE IIB               3                96
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  ZNF780A MUTATED     0   1     4
  ZNF780A WILD-TYPE   5  12   114
D121V4, multiclass
       clus
vv      ZNF780A MUTATED ZNF780A WILD-TYPE
  T1                  0                 5
  T2                  1                12
  T3+T4               4               114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V5, binary
                   cls
clus                  0   1
  ZNF780A MUTATED     1   4
  ZNF780A WILD-TYPE  31 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      1    4
  ZNF780A WILD-TYPE   31  100
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               1                31
  1               4               100
[1] 2 2
[1] FALSE
D121V6, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    2  0
  ZNF780A WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      2    0
  ZNF780A WILD-TYPE   60    3
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D121V7, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    3  2
  ZNF780A WILD-TYPE 59 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      3    2
  ZNF780A WILD-TYPE   59   72
        clus
vv       ZNF780A MUTATED ZNF780A WILD-TYPE
  FEMALE               3                59
  MALE                 2                72
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF780A MUTATED                                     4
  ZNF780A WILD-TYPE                                 118
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF780A MUTATED                                       1
  ZNF780A WILD-TYPE                                    10
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF780A MUTATED                                                  0
  ZNF780A WILD-TYPE                                                2
D121V8, multiclass
                                                  clus
vv                                                 ZNF780A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ZNF780A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V9, continuous
D121V10, continuous
                   vv
clus                R0 R1 R2 RX
  ZNF780A MUTATED    3  2  0  0
  ZNF780A WILD-TYPE 74 46  1  3
D121V11, multiclass
    clus
vv   ZNF780A MUTATED ZNF780A WILD-TYPE
  R0               3                74
  R1               2                46
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780A MUTATED       0                         0     5
  ZNF780A WILD-TYPE     2                         5   120
D121V13, multiclass
                           clus
vv                          ZNF780A MUTATED ZNF780A WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V14, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    0  5
  ZNF780A WILD-TYPE  3 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      0    5
  ZNF780A WILD-TYPE    3   99
                        clus
vv                       ZNF780A MUTATED ZNF780A WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5                99
[1] 2 2
[1] FALSE

Clustering(122) Variable = DDX4 MUTATION ANALYSIS
D122V1, survival
                sevent
clus2             0  1
  DDX4 MUTATED    2  3
  DDX4 WILD-TYPE 60 69
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            129 
  DDX4 MUTATED DDX4 WILD-TYPE 
             3             69 
$`DDX4 MUTATED`
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7885 
       20.19        17.03         1.08        19.82        41.33 

$`DDX4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 
        1.02        12.89        13.84        19.50         0.13        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        15.35        23.80         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  DDX4 MUTATED DDX4 WILD-TYPE 
          1.08           0.13 
  DDX4 MUTATED DDX4 WILD-TYPE 
         41.33          75.12 
  DDX4 MUTATED DDX4 WILD-TYPE 
         19.82          13.32 
[1] "1.1 - 41.3 (19.8)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.2"
D122V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DDX4 MUTATED          0        0         0         5         0        0
  DDX4 WILD-TYPE        4        6        20        94         4        3
D122V3, multiclass
           clus
vv          DDX4 MUTATED DDX4 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  DDX4 MUTATED     0   0     5
  DDX4 WILD-TYPE   5  13   113
D122V4, multiclass
       clus
vv      DDX4 MUTATED DDX4 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V5, binary
                cls
clus              0  1
  DDX4 MUTATED    0  5
  DDX4 WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      0    5
  DDX4 WILD-TYPE   32   99
   clus
vv  DDX4 MUTATED DDX4 WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D122V6, binary
                cls
clus              0  1
  DDX4 MUTATED    2  0
  DDX4 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      2    0
  DDX4 WILD-TYPE   60    3
   clus
vv  DDX4 MUTATED DDX4 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D122V7, binary
                cls
clus              0  1
  DDX4 MUTATED    3  2
  DDX4 WILD-TYPE 59 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      3    2
  DDX4 WILD-TYPE   59   72
        clus
vv       DDX4 MUTATED DDX4 WILD-TYPE
  FEMALE            3             59
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DDX4 MUTATED                                     4
  DDX4 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DDX4 MUTATED                                       1
  DDX4 WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DDX4 MUTATED                                                  0
  DDX4 WILD-TYPE                                                2
D122V8, multiclass
                                                  clus
vv                                                 DDX4 MUTATED DDX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V9, continuous
D122V10, continuous
                vv
clus             R0 R1 R2 RX
  DDX4 MUTATED    4  0  0  1
  DDX4 WILD-TYPE 73 48  1  2
D122V11, multiclass
    clus
vv   DDX4 MUTATED DDX4 WILD-TYPE
  R0            4             73
  R1            0             48
  R2            0              1
  RX            1              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX4 MUTATED       0                         1     4
  DDX4 WILD-TYPE     2                         4   121
D122V13, multiclass
                           clus
vv                          DDX4 MUTATED DDX4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V14, binary
                cls
clus              0  1
  DDX4 MUTATED    0  5
  DDX4 WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      0    5
  DDX4 WILD-TYPE    3   99
                        clus
vv                       DDX4 MUTATED DDX4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             99
[1] 2 2
[1] FALSE

Clustering(123) Variable = BTN2A1 MUTATION ANALYSIS
D123V1, survival
                  sevent
clus2               0  1
  BTN2A1 MUTATED    2  1
  BTN2A1 WILD-TYPE 60 71
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              131 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               71 
$`BTN2A1 MUTATED`
TCGA-3A-A9IH TCGA-HZ-A4BK TCGA-IB-7651 
       28.73        21.60        19.82 

$`BTN2A1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           19.82             0.13 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           28.73            75.12 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           21.60            13.32 
[1] "19.8 - 28.7 (21.6)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "3"  
D123V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BTN2A1 MUTATED          1        0         0         2         0        0
  BTN2A1 WILD-TYPE        3        6        20        97         4        3
D123V3, multiclass
           clus
vv          BTN2A1 MUTATED BTN2A1 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  BTN2A1 MUTATED     1   0     2
  BTN2A1 WILD-TYPE   4  13   116
D123V4, multiclass
       clus
vv      BTN2A1 MUTATED BTN2A1 WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              2              116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V5, binary
                  cls
clus                 0   1
  BTN2A1 MUTATED     1   2
  BTN2A1 WILD-TYPE  31 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      1    2
  BTN2A1 WILD-TYPE   31  102
   clus
vv  BTN2A1 MUTATED BTN2A1 WILD-TYPE
  0              1               31
  1              2              102
[1] 2 2
[1] FALSE
D123V6, binary
                  cls
clus                0  1
  BTN2A1 MUTATED    1  0
  BTN2A1 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      1    0
  BTN2A1 WILD-TYPE   61    3
   clus
vv  BTN2A1 MUTATED BTN2A1 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D123V7, binary
                  cls
clus                0  1
  BTN2A1 MUTATED    2  1
  BTN2A1 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      2    1
  BTN2A1 WILD-TYPE   60   73
        clus
vv       BTN2A1 MUTATED BTN2A1 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BTN2A1 MUTATED                                     2
  BTN2A1 WILD-TYPE                                 120
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BTN2A1 MUTATED                                       1
  BTN2A1 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BTN2A1 MUTATED                                                  0
  BTN2A1 WILD-TYPE                                                2
D123V8, multiclass
                                                  clus
vv                                                 BTN2A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 BTN2A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V9, continuous
[1] "Remove cluster labels:" "BTN2A1 MUTATED"        
clus
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
D123V10, continuous
[1] "Remove cluster labels:" "BTN2A1 MUTATED"        
clus
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  BTN2A1 MUTATED    2  1  0  0
  BTN2A1 WILD-TYPE 75 47  1  3
D123V11, multiclass
    clus
vv   BTN2A1 MUTATED BTN2A1 WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTN2A1 MUTATED       0                         0     3
  BTN2A1 WILD-TYPE     2                         5   122
D123V13, multiclass
                           clus
vv                          BTN2A1 MUTATED BTN2A1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V14, binary
                  cls
clus                 0   1
  BTN2A1 MUTATED     0   3
  BTN2A1 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      0    3
  BTN2A1 WILD-TYPE    3  101
                        clus
vv                       BTN2A1 MUTATED BTN2A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(124) Variable = TDRD5 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2              0  1
  TDRD5 MUTATED    0  4
  TDRD5 WILD-TYPE 62 68
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             130 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4              68 
$`TDRD5 MUTATED`
TCGA-HZ-7926 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-AAUO 
       17.03        12.95        19.82         7.86 

$`TDRD5 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 
       21.60         5.26        10.85         1.08         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  TDRD5 MUTATED TDRD5 WILD-TYPE 
           7.86            0.13 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
          19.82           75.12 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
         14.990          13.745 
[1] "7.9 - 19.8 (15.0)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.1"
D124V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TDRD5 MUTATED          0        0         0         3         0        1
  TDRD5 WILD-TYPE        4        6        20        96         4        2
D124V3, multiclass
           clus
vv          TDRD5 MUTATED TDRD5 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TDRD5 MUTATED     0   0     4
  TDRD5 WILD-TYPE   5  13   114
D124V4, multiclass
       clus
vv      TDRD5 MUTATED TDRD5 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V5, binary
                 cls
clus                0   1
  TDRD5 MUTATED     0   4
  TDRD5 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      0    4
  TDRD5 WILD-TYPE   32  100
   clus
vv  TDRD5 MUTATED TDRD5 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D124V6, binary
                 cls
clus               0  1
  TDRD5 MUTATED    2  1
  TDRD5 WILD-TYPE 60  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      2    1
  TDRD5 WILD-TYPE   60    2
   clus
vv  TDRD5 MUTATED TDRD5 WILD-TYPE
  0             2              60
  1             1               2
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus               0  1
  TDRD5 MUTATED    3  1
  TDRD5 WILD-TYPE 59 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      3    1
  TDRD5 WILD-TYPE   59   73
        clus
vv       TDRD5 MUTATED TDRD5 WILD-TYPE
  FEMALE             3              59
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TDRD5 MUTATED                                     4
  TDRD5 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TDRD5 MUTATED                                       0
  TDRD5 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TDRD5 MUTATED                                                  0
  TDRD5 WILD-TYPE                                                2
D124V8, multiclass
                                                  clus
vv                                                 TDRD5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TDRD5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V9, continuous
[1] "Remove cluster labels:" "TDRD5 MUTATED"         
clus
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7649 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
D124V10, continuous
[1] "Remove cluster labels:" "TDRD5 MUTATED"         
clus
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-YY-A8LH 
"TDRD5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TDRD5 MUTATED    1  2  0  1
  TDRD5 WILD-TYPE 76 46  1  2
D124V11, multiclass
    clus
vv   TDRD5 MUTATED TDRD5 WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TDRD5 MUTATED       0                         1     3
  TDRD5 WILD-TYPE     2                         4   122
D124V13, multiclass
                           clus
vv                          TDRD5 MUTATED TDRD5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V14, binary
                 cls
clus                0   1
  TDRD5 MUTATED     0   4
  TDRD5 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      0    4
  TDRD5 WILD-TYPE    3  100
                        clus
vv                       TDRD5 MUTATED TDRD5 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(125) Variable = OR2A14 MUTATION ANALYSIS
D125V1, survival
                  sevent
clus2               0  1
  OR2A14 MUTATED    2  1
  OR2A14 WILD-TYPE 60 71
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               3              131 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               1               71 
$`OR2A14 MUTATED`
TCGA-3A-A9J0 TCGA-HZ-7926 TCGA-IB-7885 
       12.39        17.03        41.33 

$`OR2A14 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        34.09        10.13        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 
        4.77        21.90        15.35        19.82        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  OR2A14 MUTATED OR2A14 WILD-TYPE 
           12.39             0.13 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
           41.33            75.12 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
           17.03            13.68 
[1] "12.4 - 41.3 (17.0)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "2.4"
D125V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR2A14 MUTATED          0        0         0         3         0        0
  OR2A14 WILD-TYPE        4        6        20        96         4        3
D125V3, multiclass
           clus
vv          OR2A14 MUTATED OR2A14 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  OR2A14 MUTATED     0   0     3
  OR2A14 WILD-TYPE   5  13   115
D125V4, multiclass
       clus
vv      OR2A14 MUTATED OR2A14 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V5, binary
                  cls
clus                 0   1
  OR2A14 MUTATED     0   3
  OR2A14 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      0    3
  OR2A14 WILD-TYPE   32  101
   clus
vv  OR2A14 MUTATED OR2A14 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D125V6, binary
                  cls
clus                0  1
  OR2A14 MUTATED    1  0
  OR2A14 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      1    0
  OR2A14 WILD-TYPE   61    3
   clus
vv  OR2A14 MUTATED OR2A14 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D125V7, binary
                  cls
clus                0  1
  OR2A14 MUTATED    1  2
  OR2A14 WILD-TYPE 61 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      1    2
  OR2A14 WILD-TYPE   61   72
        clus
vv       OR2A14 MUTATED OR2A14 WILD-TYPE
  FEMALE              1               61
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR2A14 MUTATED                                     3
  OR2A14 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR2A14 MUTATED                                       0
  OR2A14 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR2A14 MUTATED                                                  0
  OR2A14 WILD-TYPE                                                2
D125V8, multiclass
                                                  clus
vv                                                 OR2A14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 OR2A14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V9, continuous
[1] "Remove cluster labels:" "OR2A14 MUTATED"        
clus
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7886       TCGA-IB-7887 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
D125V10, continuous
[1] "Remove cluster labels:" "OR2A14 MUTATED"        
clus
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7886 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"OR2A14 WILD-TYPE" "OR2A14 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OR2A14 MUTATED    2  0  0  1
  OR2A14 WILD-TYPE 75 48  1  2
D125V11, multiclass
    clus
vv   OR2A14 MUTATED OR2A14 WILD-TYPE
  R0              2               75
  R1              0               48
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2A14 MUTATED       0                         1     2
  OR2A14 WILD-TYPE     2                         4   123
D125V13, multiclass
                           clus
vv                          OR2A14 MUTATED OR2A14 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  2              123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V14, binary
                  cls
clus                 0   1
  OR2A14 MUTATED     0   3
  OR2A14 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      0    3
  OR2A14 WILD-TYPE    3  101
                        clus
vv                       OR2A14 MUTATED OR2A14 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(126) Variable = PBRM1 MUTATION ANALYSIS
D126V1, survival
                 sevent
clus2              0  1
  PBRM1 MUTATED    2  3
  PBRM1 WILD-TYPE 60 69
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             129 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              3              69 
$`PBRM1 MUTATED`
TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7651 TCGA-LB-A7SX TCGA-Z5-AAPL 
        0.23        49.38        19.82        12.92         0.69 

$`PBRM1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
        6.38        21.60         5.26        10.85         1.08        12.95 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.40         9.44         8.05        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.23            0.13 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          49.38           75.12 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          12.92           13.81 
[1] "0.2 - 49.4 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1"  
D126V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PBRM1 MUTATED          0        1         1         3         0        0
  PBRM1 WILD-TYPE        4        5        19        96         4        3
D126V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             1              19
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PBRM1 MUTATED     0   1     4
  PBRM1 WILD-TYPE   5  12   114
D126V4, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V5, binary
                 cls
clus                0   1
  PBRM1 MUTATED     2   3
  PBRM1 WILD-TYPE  30 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      2    3
  PBRM1 WILD-TYPE   30  101
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             2              30
  1             3             101
[1] 2 2
[1] FALSE
D126V6, binary
                 cls
clus               0  1
  PBRM1 MUTATED    3  0
  PBRM1 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      3    0
  PBRM1 WILD-TYPE   59    3
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D126V7, binary
                 cls
clus               0  1
  PBRM1 MUTATED    4  1
  PBRM1 WILD-TYPE 58 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4    1
  PBRM1 WILD-TYPE   58   73
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             4              58
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PBRM1 MUTATED                                     5
  PBRM1 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PBRM1 MUTATED                                       0
  PBRM1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PBRM1 MUTATED                                                  0
  PBRM1 WILD-TYPE                                                2
D126V8, multiclass
                                                  clus
vv                                                 PBRM1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PBRM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V9, continuous
D126V10, continuous
                 vv
clus              R0 R1 R2 RX
  PBRM1 MUTATED    4  1  0  0
  PBRM1 WILD-TYPE 73 47  1  3
D126V11, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       0                         1     3
  PBRM1 WILD-TYPE     2                         4   122
D126V13, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V14, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0   4
  PBRM1 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0    4
  PBRM1 WILD-TYPE    3  100
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(127) Variable = SEPT2 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2              0  1
  SEPT2 MUTATED    0  3
  SEPT2 WILD-TYPE 62 69
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             131 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3              69 
$`SEPT2 MUTATED`
TCGA-HZ-7926 TCGA-IB-7649 TCGA-IB-7651 
       17.03        15.35        19.82 

$`SEPT2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       49.38         4.77        21.90        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SEPT2 MUTATED SEPT2 WILD-TYPE 
          15.35            0.13 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          19.82           75.12 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          17.03           13.32 
[1] "15.3 - 19.8 (17.0)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.7"
D127V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SEPT2 MUTATED          0        0         0         3         0        0
  SEPT2 WILD-TYPE        4        6        20        96         4        3
D127V3, multiclass
           clus
vv          SEPT2 MUTATED SEPT2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SEPT2 MUTATED     0   0     3
  SEPT2 WILD-TYPE   5  13   115
D127V4, multiclass
       clus
vv      SEPT2 MUTATED SEPT2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V5, binary
                 cls
clus                0   1
  SEPT2 MUTATED     0   3
  SEPT2 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      0    3
  SEPT2 WILD-TYPE   32  101
   clus
vv  SEPT2 MUTATED SEPT2 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D127V6, binary
                 cls
clus               0  1
  SEPT2 MUTATED    2  0
  SEPT2 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      2    0
  SEPT2 WILD-TYPE   60    3
   clus
vv  SEPT2 MUTATED SEPT2 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D127V7, binary
                 cls
clus               0  1
  SEPT2 MUTATED    2  1
  SEPT2 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      2    1
  SEPT2 WILD-TYPE   60   73
        clus
vv       SEPT2 MUTATED SEPT2 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEPT2 MUTATED                                     3
  SEPT2 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEPT2 MUTATED                                       0
  SEPT2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEPT2 MUTATED                                                  0
  SEPT2 WILD-TYPE                                                2
D127V8, multiclass
                                                  clus
vv                                                 SEPT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SEPT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V9, continuous
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
D127V10, continuous
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-YY-A8LH 
"SEPT2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SEPT2 MUTATED    1  1  0  1
  SEPT2 WILD-TYPE 76 47  1  2
D127V11, multiclass
    clus
vv   SEPT2 MUTATED SEPT2 WILD-TYPE
  R0             1              76
  R1             1              47
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEPT2 MUTATED       0                         1     1
  SEPT2 WILD-TYPE     2                         4   124
D127V13, multiclass
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2             130 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-2J-AAB9      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-2J-AABH      TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-2J-AABU      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-2L-AAQI      TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I5 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-3A-A9I7      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-3A-A9IH      TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-6879 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-F2-A44H      TCGA-F2-A7TX      TCGA-F2-A8YN 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A545      TCGA-FB-A5VM 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-7919 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-7922      TCGA-HZ-7925      TCGA-HZ-8001      TCGA-HZ-8002 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-8003      TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-8519      TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A49H      TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7646      TCGA-IB-7647 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7891      TCGA-IB-7893 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7897      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-US-A776      TCGA-US-A779 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-US-A77E      TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XD-AAUL      TCGA-YB-A89D      TCGA-YH-A8SY 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
D127V14, binary
                 cls
clus                0   1
  SEPT2 MUTATED     0   2
  SEPT2 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      0    2
  SEPT2 WILD-TYPE    3  102
                        clus
vv                       SEPT2 MUTATED SEPT2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(128) Variable = WDHD1 MUTATION ANALYSIS
D128V1, survival
                 sevent
clus2              0  1
  WDHD1 MUTATED    0  3
  WDHD1 WILD-TYPE 62 69
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             131 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3              69 
$`WDHD1 MUTATED`
TCGA-HZ-8005 TCGA-HZ-A49I TCGA-IB-7651 
        3.95        10.13        19.82 

$`WDHD1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        17.92        21.70        16.14         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  WDHD1 MUTATED WDHD1 WILD-TYPE 
           3.95            0.13 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
          19.82           75.12 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
          10.13           13.81 
[1] "4.0 - 19.8 (10.1)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.9"
D128V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WDHD1 MUTATED          0        0         0         3         0        0
  WDHD1 WILD-TYPE        4        6        20        96         4        3
D128V3, multiclass
           clus
vv          WDHD1 MUTATED WDHD1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  WDHD1 MUTATED     0   0     3
  WDHD1 WILD-TYPE   5  13   115
D128V4, multiclass
       clus
vv      WDHD1 MUTATED WDHD1 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V5, binary
                 cls
clus                0   1
  WDHD1 MUTATED     0   3
  WDHD1 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      0    3
  WDHD1 WILD-TYPE   32  101
   clus
vv  WDHD1 MUTATED WDHD1 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D128V6, binary
                 cls
clus               0  1
  WDHD1 MUTATED    1  0
  WDHD1 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      1    0
  WDHD1 WILD-TYPE   61    3
   clus
vv  WDHD1 MUTATED WDHD1 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D128V7, binary
                 cls
clus               0  1
  WDHD1 MUTATED    1  2
  WDHD1 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      1    2
  WDHD1 WILD-TYPE   61   72
        clus
vv       WDHD1 MUTATED WDHD1 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDHD1 MUTATED                                     3
  WDHD1 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDHD1 MUTATED                                       0
  WDHD1 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDHD1 MUTATED                                                  0
  WDHD1 WILD-TYPE                                                2
D128V8, multiclass
                                                  clus
vv                                                 WDHD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 WDHD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V9, continuous
[1] "Remove cluster labels:" "WDHD1 MUTATED"         
clus
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
D128V10, continuous
[1] "Remove cluster labels:" "WDHD1 MUTATED"         
clus
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  WDHD1 MUTATED    1  2  0  0
  WDHD1 WILD-TYPE 76 46  1  3
D128V11, multiclass
    clus
vv   WDHD1 MUTATED WDHD1 WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDHD1 MUTATED       0                         0     3
  WDHD1 WILD-TYPE     2                         5   122
D128V13, multiclass
                           clus
vv                          WDHD1 MUTATED WDHD1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V14, binary
                 cls
clus                0   1
  WDHD1 MUTATED     0   3
  WDHD1 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      0    3
  WDHD1 WILD-TYPE    3  101
                        clus
vv                       WDHD1 MUTATED WDHD1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(129) Variable = ANKRD49 MUTATION ANALYSIS
D129V1, survival
                   sevent
clus2                0  1
  ANKRD49 MUTATED    0  3
  ANKRD49 WILD-TYPE 62 69
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               131 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3                69 
$`ANKRD49 MUTATED`
TCGA-HZ-8005 TCGA-IB-7651 TCGA-IB-7887 
        3.95        19.82         3.62 

$`ANKRD49 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
             3.62              0.13 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
            19.82             75.12 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
             3.95             13.81 
[1] "3.6 - 19.8 (4.0)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.7"
D129V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANKRD49 MUTATED          0        0         0         3         0        0
  ANKRD49 WILD-TYPE        4        6        20        96         4        3
D129V3, multiclass
           clus
vv          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               3                96
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  ANKRD49 MUTATED     0   0     3
  ANKRD49 WILD-TYPE   5  13   115
D129V4, multiclass
       clus
vv      ANKRD49 MUTATED ANKRD49 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V5, binary
                   cls
clus                  0   1
  ANKRD49 MUTATED     0   3
  ANKRD49 WILD-TYPE  32 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      0    3
  ANKRD49 WILD-TYPE   32  101
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               0                32
  1               3               101
[1] 2 2
[1] FALSE
D129V6, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  0
  ANKRD49 WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    0
  ANKRD49 WILD-TYPE   60    3
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D129V7, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  1
  ANKRD49 WILD-TYPE 60 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    1
  ANKRD49 WILD-TYPE   60   73
        clus
vv       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  FEMALE               2                60
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD49 MUTATED                                     3
  ANKRD49 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD49 MUTATED                                       0
  ANKRD49 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD49 MUTATED                                                  0
  ANKRD49 WILD-TYPE                                                2
D129V8, multiclass
                                                  clus
vv                                                 ANKRD49 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ANKRD49 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V9, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7891 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
D129V10, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                1                38 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ANKRD49 MUTATED    1  2  0  0
  ANKRD49 WILD-TYPE 76 46  1  3
D129V11, multiclass
    clus
vv   ANKRD49 MUTATED ANKRD49 WILD-TYPE
  R0               1                76
  R1               2                46
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD49 MUTATED       0                         0     3
  ANKRD49 WILD-TYPE     2                         5   122
D129V13, multiclass
                           clus
vv                          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V14, binary
                   cls
clus                  0   1
  ANKRD49 MUTATED     0   3
  ANKRD49 WILD-TYPE   3 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      0    3
  ANKRD49 WILD-TYPE    3  101
                        clus
vv                       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               101
[1] 2 2
[1] FALSE

Clustering(130) Variable = PAPSS2 MUTATION ANALYSIS
D130V1, survival
                  sevent
clus2               0  1
  PAPSS2 MUTATED    2  2
  PAPSS2 WILD-TYPE 60 70
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              130 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               2               70 
$`PAPSS2 MUTATED`
TCGA-HZ-A4BK TCGA-IB-7651 TCGA-IB-7887 TCGA-Q3-A5QY 
       21.60        19.82         3.62        13.68 

$`PAPSS2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
            3.62             0.13 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
           21.60            75.12 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
          16.750           13.565 
[1] "3.6 - 21.6 (16.8)" "0.1 - 75.1 (13.6)"
[1] "hr=" "1"  
D130V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PAPSS2 MUTATED          0        0         0         4         0        0
  PAPSS2 WILD-TYPE        4        6        20        95         4        3
D130V3, multiclass
           clus
vv          PAPSS2 MUTATED PAPSS2 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PAPSS2 MUTATED     0   0     4
  PAPSS2 WILD-TYPE   5  13   114
D130V4, multiclass
       clus
vv      PAPSS2 MUTATED PAPSS2 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V5, binary
                  cls
clus                 0   1
  PAPSS2 MUTATED     0   4
  PAPSS2 WILD-TYPE  32 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      0    4
  PAPSS2 WILD-TYPE   32  100
   clus
vv  PAPSS2 MUTATED PAPSS2 WILD-TYPE
  0              0               32
  1              4              100
[1] 2 2
[1] FALSE
D130V6, binary
                  cls
clus                0  1
  PAPSS2 MUTATED    2  0
  PAPSS2 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      2    0
  PAPSS2 WILD-TYPE   60    3
   clus
vv  PAPSS2 MUTATED PAPSS2 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D130V7, binary
                  cls
clus                0  1
  PAPSS2 MUTATED    2  2
  PAPSS2 WILD-TYPE 60 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      2    2
  PAPSS2 WILD-TYPE   60   72
        clus
vv       PAPSS2 MUTATED PAPSS2 WILD-TYPE
  FEMALE              2               60
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PAPSS2 MUTATED                                     3
  PAPSS2 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PAPSS2 MUTATED                                       1
  PAPSS2 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PAPSS2 MUTATED                                                  0
  PAPSS2 WILD-TYPE                                                2
D130V8, multiclass
                                                  clus
vv                                                 PAPSS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 PAPSS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V9, continuous
[1] "Remove cluster labels:" "PAPSS2 MUTATED"        
clus
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
D130V10, continuous
[1] "Remove cluster labels:" "PAPSS2 MUTATED"        
clus
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PAPSS2 MUTATED    2  2  0  0
  PAPSS2 WILD-TYPE 75 46  1  3
D130V11, multiclass
    clus
vv   PAPSS2 MUTATED PAPSS2 WILD-TYPE
  R0              2               75
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAPSS2 MUTATED       0                         0     4
  PAPSS2 WILD-TYPE     2                         5   121
D130V13, multiclass
                           clus
vv                          PAPSS2 MUTATED PAPSS2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V14, binary
                  cls
clus                 0   1
  PAPSS2 MUTATED     0   4
  PAPSS2 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      0    4
  PAPSS2 WILD-TYPE    3  100
                        clus
vv                       PAPSS2 MUTATED PAPSS2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(131) Variable = GPRC6A MUTATION ANALYSIS
D131V1, survival
                  sevent
clus2               0  1
  GPRC6A MUTATED    2  3
  GPRC6A WILD-TYPE 60 69
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              129 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               3               69 
$`GPRC6A MUTATED`
TCGA-3E-AAAZ TCGA-HZ-8001 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
       71.74        23.21        15.35        19.82        41.33 

$`GPRC6A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
        4.77        21.90        23.80         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  GPRC6A MUTATED GPRC6A WILD-TYPE 
           15.35             0.13 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
           71.74            75.12 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
           23.21            12.99 
[1] "15.3 - 71.7 (23.2)" "0.1 - 75.1 (13.0)" 
[1] "hr=" "2.2"
D131V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPRC6A MUTATED          0        0         1         3         1        0
  GPRC6A WILD-TYPE        4        6        19        96         3        3
D131V3, multiclass
           clus
vv          GPRC6A MUTATED GPRC6A WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              3               96
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  GPRC6A MUTATED     0   0     5
  GPRC6A WILD-TYPE   5  13   113
D131V4, multiclass
       clus
vv      GPRC6A MUTATED GPRC6A WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V5, binary
                  cls
clus                 0   1
  GPRC6A MUTATED     2   3
  GPRC6A WILD-TYPE  30 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      2    3
  GPRC6A WILD-TYPE   30  101
   clus
vv  GPRC6A MUTATED GPRC6A WILD-TYPE
  0              2               30
  1              3              101
[1] 2 2
[1] FALSE
D131V6, binary
                  cls
clus                0  1
  GPRC6A MUTATED    3  0
  GPRC6A WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      3    0
  GPRC6A WILD-TYPE   59    3
   clus
vv  GPRC6A MUTATED GPRC6A WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D131V7, binary
                  cls
clus                0  1
  GPRC6A MUTATED    3  2
  GPRC6A WILD-TYPE 59 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      3    2
  GPRC6A WILD-TYPE   59   72
        clus
vv       GPRC6A MUTATED GPRC6A WILD-TYPE
  FEMALE              3               59
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPRC6A MUTATED                                     5
  GPRC6A WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPRC6A MUTATED                                       0
  GPRC6A WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPRC6A MUTATED                                                  0
  GPRC6A WILD-TYPE                                                2
D131V8, multiclass
                                                  clus
vv                                                 GPRC6A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 GPRC6A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V9, continuous
D131V10, continuous
                  vv
clus               R0 R1 R2 RX
  GPRC6A MUTATED    3  1  0  0
  GPRC6A WILD-TYPE 74 47  1  3
D131V11, multiclass
    clus
vv   GPRC6A MUTATED GPRC6A WILD-TYPE
  R0              3               74
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPRC6A MUTATED       0                         0     4
  GPRC6A WILD-TYPE     2                         5   121
D131V13, multiclass
                           clus
vv                          GPRC6A MUTATED GPRC6A WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V14, binary
                  cls
clus                 0   1
  GPRC6A MUTATED     1   3
  GPRC6A WILD-TYPE   2 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      1    3
  GPRC6A WILD-TYPE    2  101
                        clus
vv                       GPRC6A MUTATED GPRC6A WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(132) Variable = PDXDC1 MUTATION ANALYSIS
D132V1, survival
                  sevent
clus2               0  1
  PDXDC1 MUTATED    1  2
  PDXDC1 WILD-TYPE 61 70
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              131 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               2               70 
$`PDXDC1 MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ3 TCGA-IB-7651 
       23.54         1.02        19.82 

$`PDXDC1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 
       12.53        34.82        15.55         4.04         5.03        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
            1.02             0.13 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
           23.54            75.12 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
           19.82            13.68 
[1] "1.0 - 23.5 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D132V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PDXDC1 MUTATED          0        0         0         3         0        0
  PDXDC1 WILD-TYPE        4        6        20        96         4        3
D132V3, multiclass
           clus
vv          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PDXDC1 MUTATED     0   1     2
  PDXDC1 WILD-TYPE   5  12   116
D132V4, multiclass
       clus
vv      PDXDC1 MUTATED PDXDC1 WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              2              116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V5, binary
                  cls
clus                 0   1
  PDXDC1 MUTATED     0   3
  PDXDC1 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE   32  101
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D132V6, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    1  0
  PDXDC1 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      1    0
  PDXDC1 WILD-TYPE   61    3
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D132V7, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    2  1
  PDXDC1 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      2    1
  PDXDC1 WILD-TYPE   60   73
        clus
vv       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDXDC1 MUTATED                                     3
  PDXDC1 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDXDC1 MUTATED                                       0
  PDXDC1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDXDC1 MUTATED                                                  0
  PDXDC1 WILD-TYPE                                                2
D132V8, multiclass
                                                  clus
vv                                                 PDXDC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 PDXDC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V9, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
D132V10, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PDXDC1 MUTATED    3  0  0  0
  PDXDC1 WILD-TYPE 74 48  1  3
D132V11, multiclass
    clus
vv   PDXDC1 MUTATED PDXDC1 WILD-TYPE
  R0              3               74
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDXDC1 MUTATED       0                         0     3
  PDXDC1 WILD-TYPE     2                         5   122
D132V13, multiclass
                           clus
vv                          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V14, binary
                  cls
clus                 0   1
  PDXDC1 MUTATED     0   3
  PDXDC1 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE    3  101
                        clus
vv                       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(133) Variable = TGM5 MUTATION ANALYSIS
D133V1, survival
                sevent
clus2             0  1
  TGM5 MUTATED    2  2
  TGM5 WILD-TYPE 60 70
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            130 
  TGM5 MUTATED TGM5 WILD-TYPE 
             2             70 
$`TGM5 MUTATED`
TCGA-2L-AAQJ TCGA-HZ-8317 TCGA-IB-8126 TCGA-Q3-A5QY 
       12.95        12.43         2.47        13.68 

$`TGM5 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 
       23.21        12.03         0.69         3.95         9.83        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  TGM5 MUTATED TGM5 WILD-TYPE 
          2.47           0.13 
  TGM5 MUTATED TGM5 WILD-TYPE 
         13.68          75.12 
  TGM5 MUTATED TGM5 WILD-TYPE 
         12.69          13.99 
[1] "2.5 - 13.7 (12.7)" "0.1 - 75.1 (14.0)"
[1] "hr=" "1.7"
D133V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TGM5 MUTATED          0        0         0         2         2        0
  TGM5 WILD-TYPE        4        6        20        97         2        3
D133V3, multiclass
           clus
vv          TGM5 MUTATED TGM5 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            2             97
  STAGE III            2              2
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  TGM5 MUTATED     0   0     4
  TGM5 WILD-TYPE   5  13   114
D133V4, multiclass
       clus
vv      TGM5 MUTATED TGM5 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V5, binary
                cls
clus               0   1
  TGM5 MUTATED     1   3
  TGM5 WILD-TYPE  31 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      1    3
  TGM5 WILD-TYPE   31  101
   clus
vv  TGM5 MUTATED TGM5 WILD-TYPE
  0            1             31
  1            3            101
[1] 2 2
[1] FALSE
D133V6, binary
                cls
clus              0  1
  TGM5 MUTATED    1  0
  TGM5 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      1    0
  TGM5 WILD-TYPE   61    3
   clus
vv  TGM5 MUTATED TGM5 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D133V7, binary
                cls
clus              0  1
  TGM5 MUTATED    3  1
  TGM5 WILD-TYPE 59 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      3    1
  TGM5 WILD-TYPE   59   73
        clus
vv       TGM5 MUTATED TGM5 WILD-TYPE
  FEMALE            3             59
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGM5 MUTATED                                     4
  TGM5 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGM5 MUTATED                                       0
  TGM5 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGM5 MUTATED                                                  0
  TGM5 WILD-TYPE                                                2
D133V8, multiclass
                                                  clus
vv                                                 TGM5 MUTATED TGM5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V9, continuous
[1] "Remove cluster labels:" "TGM5 MUTATED"          
clus
  TGM5 MUTATED TGM5 WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-7887     TCGA-IB-7891     TCGA-IB-8127     TCGA-IB-A5SS 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
D133V10, continuous
[1] "Remove cluster labels:" "TGM5 MUTATED"          
clus
  TGM5 MUTATED TGM5 WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-7886     TCGA-IB-7891     TCGA-IB-8127     TCGA-IB-A5SS 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TGM5 MUTATED    1  3  0  0
  TGM5 WILD-TYPE 76 45  1  3
D133V11, multiclass
    clus
vv   TGM5 MUTATED TGM5 WILD-TYPE
  R0            1             76
  R1            3             45
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGM5 MUTATED       0                         0     4
  TGM5 WILD-TYPE     2                         5   121
D133V13, multiclass
                           clus
vv                          TGM5 MUTATED TGM5 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V14, binary
                cls
clus               0   1
  TGM5 MUTATED     0   3
  TGM5 WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      0    3
  TGM5 WILD-TYPE    3  101
                        clus
vv                       TGM5 MUTATED TGM5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(134) Variable = NUP54 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2              0  1
  NUP54 MUTATED    0  3
  NUP54 WILD-TYPE 62 69
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             131 
  NUP54 MUTATED NUP54 WILD-TYPE 
              3              69 
$`NUP54 MUTATED`
TCGA-IB-7644 TCGA-IB-7651 TCGA-OE-A75W 
       12.95        19.82         8.78 

$`NUP54 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29        19.20        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  NUP54 MUTATED NUP54 WILD-TYPE 
           8.78            0.13 
  NUP54 MUTATED NUP54 WILD-TYPE 
          19.82           75.12 
  NUP54 MUTATED NUP54 WILD-TYPE 
          12.95           13.81 
[1] "8.8 - 19.8 (12.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.3"
D134V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NUP54 MUTATED          0        0         1         1         0        1
  NUP54 WILD-TYPE        4        6        19        98         4        2
D134V3, multiclass
           clus
vv          NUP54 MUTATED NUP54 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             1              98
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NUP54 MUTATED     0   0     3
  NUP54 WILD-TYPE   5  13   115
D134V4, multiclass
       clus
vv      NUP54 MUTATED NUP54 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V5, binary
                 cls
clus                0   1
  NUP54 MUTATED     1   2
  NUP54 WILD-TYPE  31 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      1    2
  NUP54 WILD-TYPE   31  102
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             1              31
  1             2             102
[1] 2 2
[1] FALSE
D134V6, binary
                 cls
clus               0  1
  NUP54 MUTATED    2  1
  NUP54 WILD-TYPE 60  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      2    1
  NUP54 WILD-TYPE   60    2
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             2              60
  1             1               2
[1] 2 2
[1] FALSE
D134V7, binary
                 cls
clus               0  1
  NUP54 MUTATED    2  1
  NUP54 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      2    1
  NUP54 WILD-TYPE   60   73
        clus
vv       NUP54 MUTATED NUP54 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NUP54 MUTATED                                     3
  NUP54 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NUP54 MUTATED                                       0
  NUP54 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NUP54 MUTATED                                                  0
  NUP54 WILD-TYPE                                                2
D134V8, multiclass
                                                  clus
vv                                                 NUP54 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NUP54 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V9, continuous
D134V10, continuous
                 vv
clus              R0 R1 R2 RX
  NUP54 MUTATED    2  1  0  0
  NUP54 WILD-TYPE 75 47  1  3
D134V11, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP54 MUTATED       0                         0     3
  NUP54 WILD-TYPE     2                         5   122
D134V13, multiclass
                           clus
vv                          NUP54 MUTATED NUP54 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V14, binary
                 cls
clus                0   1
  NUP54 MUTATED     0   3
  NUP54 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      0    3
  NUP54 WILD-TYPE    3  101
                        clus
vv                       NUP54 MUTATED NUP54 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(135) Variable = NLRP6 MUTATION ANALYSIS
D135V1, survival
                 sevent
clus2              0  1
  NLRP6 MUTATED    0  3
  NLRP6 WILD-TYPE 62 69
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             131 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3              69 
$`NLRP6 MUTATED`
TCGA-FB-AAQ1 TCGA-OE-A75W TCGA-US-A774 
        4.04         8.78        22.85 

$`NLRP6 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        23.54        15.55         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 
       15.32         9.40        21.24        17.26        23.08        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
           4.04            0.13 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          22.85           75.12 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
           8.78           13.81 
[1] "4.0 - 22.9 (8.8)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.3"
D135V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NLRP6 MUTATED          0        0         1         2         0        0
  NLRP6 WILD-TYPE        4        6        19        97         4        3
D135V3, multiclass
           clus
vv          NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NLRP6 MUTATED     0   0     3
  NLRP6 WILD-TYPE   5  13   115
D135V4, multiclass
       clus
vv      NLRP6 MUTATED NLRP6 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V5, binary
                 cls
clus                0   1
  NLRP6 MUTATED     1   2
  NLRP6 WILD-TYPE  31 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE   31  102
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1              31
  1             2             102
[1] 2 2
[1] FALSE
D135V6, binary
                 cls
clus               0  1
  NLRP6 MUTATED    1  0
  NLRP6 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    0
  NLRP6 WILD-TYPE   61    3
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D135V7, binary
                 cls
clus               0  1
  NLRP6 MUTATED    1  2
  NLRP6 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE   61   72
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NLRP6 MUTATED                                     3
  NLRP6 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NLRP6 MUTATED                                       0
  NLRP6 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NLRP6 MUTATED                                                  0
  NLRP6 WILD-TYPE                                                2
D135V8, multiclass
                                                  clus
vv                                                 NLRP6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NLRP6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V9, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-S4-A8RM      TCGA-S4-A8RP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
D135V10, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-S4-A8RM      TCGA-XD-AAUI      TCGA-XD-AAUL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-YY-A8LH 
"NLRP6 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NLRP6 MUTATED    2  1  0  0
  NLRP6 WILD-TYPE 75 47  1  3
D135V11, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED       0                         0     3
  NLRP6 WILD-TYPE     2                         5   122
D135V13, multiclass
                           clus
vv                          NLRP6 MUTATED NLRP6 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V14, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   3
  NLRP6 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    3
  NLRP6 WILD-TYPE    3  101
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(136) Variable = DHX35 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2              0  1
  DHX35 MUTATED    2  2
  DHX35 WILD-TYPE 60 70
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             130 
  DHX35 MUTATED DHX35 WILD-TYPE 
              2              70 
$`DHX35 MUTATED`
TCGA-2J-AAB1 TCGA-FB-A5VM TCGA-IB-7885 TCGA-IB-7887 
        2.17        14.76        41.33         3.62 

$`DHX35 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 
        4.77        21.90        15.35        19.82        23.80         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  DHX35 MUTATED DHX35 WILD-TYPE 
           2.17            0.13 
  DHX35 MUTATED DHX35 WILD-TYPE 
          41.33           75.12 
  DHX35 MUTATED DHX35 WILD-TYPE 
          9.190          13.745 
[1] "2.2 - 41.3 (9.2)"  "0.1 - 75.1 (13.7)"
[1] "hr=" "1"  
D136V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DHX35 MUTATED          0        1         0         3         0        0
  DHX35 WILD-TYPE        4        5        20        96         4        3
D136V3, multiclass
           clus
vv          DHX35 MUTATED DHX35 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              1               5
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  DHX35 MUTATED     0   1     3
  DHX35 WILD-TYPE   5  12   115
D136V4, multiclass
       clus
vv      DHX35 MUTATED DHX35 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V5, binary
                 cls
clus                0   1
  DHX35 MUTATED     1   3
  DHX35 WILD-TYPE  31 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      1    3
  DHX35 WILD-TYPE   31  101
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             1              31
  1             3             101
[1] 2 2
[1] FALSE
D136V6, binary
                 cls
clus               0  1
  DHX35 MUTATED    4  0
  DHX35 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      4    0
  DHX35 WILD-TYPE   58    3
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             4              58
  1             0               3
[1] 2 2
[1] FALSE
D136V7, binary
                 cls
clus               0  1
  DHX35 MUTATED    2  2
  DHX35 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      2    2
  DHX35 WILD-TYPE   60   72
        clus
vv       DHX35 MUTATED DHX35 WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DHX35 MUTATED                                     3
  DHX35 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DHX35 MUTATED                                       1
  DHX35 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DHX35 MUTATED                                                  0
  DHX35 WILD-TYPE                                                2
D136V8, multiclass
                                                  clus
vv                                                 DHX35 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DHX35 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V9, continuous
D136V10, continuous
                 vv
clus              R0 R1 R2 RX
  DHX35 MUTATED    3  1  0  0
  DHX35 WILD-TYPE 74 47  1  3
D136V11, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHX35 MUTATED       0                         0     4
  DHX35 WILD-TYPE     2                         5   121
D136V13, multiclass
                           clus
vv                          DHX35 MUTATED DHX35 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V14, binary
                 cls
clus                0   1
  DHX35 MUTATED     0   3
  DHX35 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      0    3
  DHX35 WILD-TYPE    3  101
                        clus
vv                       DHX35 MUTATED DHX35 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(137) Variable = CEACAM4 MUTATION ANALYSIS
D137V1, survival
                   sevent
clus2                0  1
  CEACAM4 MUTATED    0  3
  CEACAM4 WILD-TYPE 62 69
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                3               131 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                3                69 
$`CEACAM4 MUTATED`
TCGA-2J-AAB6 TCGA-FB-AAQ2 TCGA-IB-7651 
        9.63         5.03        19.82 

$`CEACAM4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-H6-8124 
       34.82        23.54        15.55         4.04         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
             5.03              0.13 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
            19.82             75.12 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
             9.63             13.81 
[1] "5.0 - 19.8 (9.6)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "2.8"
D137V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CEACAM4 MUTATED          0        0         1         2         0        0
  CEACAM4 WILD-TYPE        4        6        19        97         4        3
D137V3, multiclass
           clus
vv          CEACAM4 MUTATED CEACAM4 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               1                19
  STAGE IIB               2                97
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  CEACAM4 MUTATED     0   0     3
  CEACAM4 WILD-TYPE   5  13   115
D137V4, multiclass
       clus
vv      CEACAM4 MUTATED CEACAM4 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V5, binary
                   cls
clus                  0   1
  CEACAM4 MUTATED     1   2
  CEACAM4 WILD-TYPE  31 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      1    2
  CEACAM4 WILD-TYPE   31  102
   clus
vv  CEACAM4 MUTATED CEACAM4 WILD-TYPE
  0               1                31
  1               2               102
[1] 2 2
[1] FALSE
D137V6, binary
                   cls
clus                 0  1
  CEACAM4 MUTATED    2  0
  CEACAM4 WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      2    0
  CEACAM4 WILD-TYPE   60    3
   clus
vv  CEACAM4 MUTATED CEACAM4 WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D137V7, binary
                   cls
clus                 0  1
  CEACAM4 MUTATED    2  1
  CEACAM4 WILD-TYPE 60 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      2    1
  CEACAM4 WILD-TYPE   60   73
        clus
vv       CEACAM4 MUTATED CEACAM4 WILD-TYPE
  FEMALE               2                60
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEACAM4 MUTATED                                     3
  CEACAM4 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEACAM4 MUTATED                                       0
  CEACAM4 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEACAM4 MUTATED                                                  0
  CEACAM4 WILD-TYPE                                                2
D137V8, multiclass
                                                  clus
vv                                                 CEACAM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 CEACAM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V9, continuous
[1] "Remove cluster labels:" "CEACAM4 MUTATED"       
clus
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                1                47 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-YY-A8LH 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
D137V10, continuous
[1] "Remove cluster labels:" "CEACAM4 MUTATED"       
clus
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                1                38 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CEACAM4 MUTATED    2  1  0  0
  CEACAM4 WILD-TYPE 75 47  1  3
D137V11, multiclass
    clus
vv   CEACAM4 MUTATED CEACAM4 WILD-TYPE
  R0               2                75
  R1               1                47
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM4 MUTATED       0                         0     3
  CEACAM4 WILD-TYPE     2                         5   122
D137V13, multiclass
                           clus
vv                          CEACAM4 MUTATED CEACAM4 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V14, binary
                   cls
clus                  0   1
  CEACAM4 MUTATED     0   2
  CEACAM4 WILD-TYPE   3 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      0    2
  CEACAM4 WILD-TYPE    3  102
                        clus
vv                       CEACAM4 MUTATED CEACAM4 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               2               102
[1] 2 2
[1] FALSE

Clustering(138) Variable = MMP13 MUTATION ANALYSIS
D138V1, survival
                 sevent
clus2              0  1
  MMP13 MUTATED    0  3
  MMP13 WILD-TYPE 62 69
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             131 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3              69 
$`MMP13 MUTATED`
TCGA-3A-A9IB TCGA-FB-AAQ1 TCGA-IB-7651 
        7.36         4.04        19.82 

$`MMP13 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       34.82        23.54        15.55         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  MMP13 MUTATED MMP13 WILD-TYPE 
           4.04            0.13 
  MMP13 MUTATED MMP13 WILD-TYPE 
          19.82           75.12 
  MMP13 MUTATED MMP13 WILD-TYPE 
           7.36           13.81 
[1] "4.0 - 19.8 (7.4)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.2"
D138V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MMP13 MUTATED          0        0         0         3         0        0
  MMP13 WILD-TYPE        4        6        20        96         4        3
D138V3, multiclass
           clus
vv          MMP13 MUTATED MMP13 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  MMP13 MUTATED     0   0     3
  MMP13 WILD-TYPE   5  13   115
D138V4, multiclass
       clus
vv      MMP13 MUTATED MMP13 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V5, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   3
  MMP13 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    3
  MMP13 WILD-TYPE   32  101
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D138V6, binary
                 cls
clus               0  1
  MMP13 MUTATED    1  0
  MMP13 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      1    0
  MMP13 WILD-TYPE   61    3
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D138V7, binary
                 cls
clus               0  1
  MMP13 MUTATED    2  1
  MMP13 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      2    1
  MMP13 WILD-TYPE   60   73
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP13 MUTATED                                     3
  MMP13 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP13 MUTATED                                       0
  MMP13 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP13 MUTATED                                                  0
  MMP13 WILD-TYPE                                                2
D138V8, multiclass
                                                  clus
vv                                                 MMP13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 MMP13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V9, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
D138V10, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-YY-A8LH 
"MMP13 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MMP13 MUTATED    2  1  0  0
  MMP13 WILD-TYPE 75 47  1  3
D138V11, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED       0                         0     3
  MMP13 WILD-TYPE     2                         5   122
D138V13, multiclass
                           clus
vv                          MMP13 MUTATED MMP13 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V14, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   3
  MMP13 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    3
  MMP13 WILD-TYPE    3  101
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(139) Variable = SYCP2 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2              0  1
  SYCP2 MUTATED    2  3
  SYCP2 WILD-TYPE 60 69
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             129 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              3              69 
$`SYCP2 MUTATED`
TCGA-F2-A7TX TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-AAUT 
        3.12        20.19        19.82        41.33         9.44 

$`SYCP2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74        10.98         7.66        19.27        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        15.35        23.80         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  SYCP2 MUTATED SYCP2 WILD-TYPE 
           3.12            0.13 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          41.33           75.12 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          19.82           13.68 
[1] "3.1 - 41.3 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D139V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SYCP2 MUTATED          0        0         0         5         0        0
  SYCP2 WILD-TYPE        4        6        20        94         4        3
D139V3, multiclass
           clus
vv          SYCP2 MUTATED SYCP2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SYCP2 MUTATED     0   1     4
  SYCP2 WILD-TYPE   5  12   114
D139V4, multiclass
       clus
vv      SYCP2 MUTATED SYCP2 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V5, binary
                 cls
clus               0  1
  SYCP2 MUTATED    0  5
  SYCP2 WILD-TYPE 32 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0    5
  SYCP2 WILD-TYPE   32   99
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             0              32
  1             5              99
[1] 2 2
[1] FALSE
D139V6, binary
                 cls
clus               0  1
  SYCP2 MUTATED    4  0
  SYCP2 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      4    0
  SYCP2 WILD-TYPE   58    3
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             4              58
  1             0               3
[1] 2 2
[1] FALSE
D139V7, binary
                 cls
clus               0  1
  SYCP2 MUTATED    2  3
  SYCP2 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      2    3
  SYCP2 WILD-TYPE   60   71
        clus
vv       SYCP2 MUTATED SYCP2 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYCP2 MUTATED                                     4
  SYCP2 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYCP2 MUTATED                                       0
  SYCP2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYCP2 MUTATED                                                  1
  SYCP2 WILD-TYPE                                                1
D139V8, multiclass
                                                  clus
vv                                                 SYCP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 SYCP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V9, continuous
D139V10, continuous
                 vv
clus              R0 R1 R2 RX
  SYCP2 MUTATED    3  2  0  0
  SYCP2 WILD-TYPE 74 46  1  3
D139V11, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  R0             3              74
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYCP2 MUTATED       0                         0     5
  SYCP2 WILD-TYPE     2                         5   120
D139V13, multiclass
                           clus
vv                          SYCP2 MUTATED SYCP2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V14, binary
                 cls
clus                0   1
  SYCP2 MUTATED     0   4
  SYCP2 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0    4
  SYCP2 WILD-TYPE    3  100
                        clus
vv                       SYCP2 MUTATED SYCP2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(140) Variable = LACTB MUTATION ANALYSIS
D140V1, survival
                 sevent
clus2              0  1
  LACTB MUTATED    1  2
  LACTB WILD-TYPE 61 70
  LACTB MUTATED LACTB WILD-TYPE 
              3             131 
  LACTB MUTATED LACTB WILD-TYPE 
              2              70 
$`LACTB MUTATED`
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
       15.35        19.82        41.33 

$`LACTB WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7886 
       12.95        49.38         4.77        21.90        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  LACTB MUTATED LACTB WILD-TYPE 
          15.35            0.13 
  LACTB MUTATED LACTB WILD-TYPE 
          41.33           75.12 
  LACTB MUTATED LACTB WILD-TYPE 
          19.82           13.32 
[1] "15.3 - 41.3 (19.8)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.3"
D140V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LACTB MUTATED          0        0         0         3         0        0
  LACTB WILD-TYPE        4        6        20        96         4        3
D140V3, multiclass
           clus
vv          LACTB MUTATED LACTB WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  LACTB MUTATED     0   0     3
  LACTB WILD-TYPE   5  13   115
D140V4, multiclass
       clus
vv      LACTB MUTATED LACTB WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V5, binary
                 cls
clus                0   1
  LACTB MUTATED     0   3
  LACTB WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      0    3
  LACTB WILD-TYPE   32  101
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D140V6, binary
                 cls
clus               0  1
  LACTB MUTATED    3  0
  LACTB WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    0
  LACTB WILD-TYPE   59    3
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D140V7, binary
                 cls
clus               0  1
  LACTB MUTATED    3  0
  LACTB WILD-TYPE 59 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    0
  LACTB WILD-TYPE   59   74
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  FEMALE             3              59
  MALE               0              74
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LACTB MUTATED                                     3
  LACTB WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LACTB MUTATED                                       0
  LACTB WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LACTB MUTATED                                                  0
  LACTB WILD-TYPE                                                2
D140V8, multiclass
                                                  clus
vv                                                 LACTB MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 LACTB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V9, continuous
D140V10, continuous
                 vv
clus              R0 R1 R2 RX
  LACTB MUTATED    2  1  0  0
  LACTB WILD-TYPE 75 47  1  3
D140V11, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LACTB MUTATED       0                         0     2
  LACTB WILD-TYPE     2                         5   123
D140V13, multiclass
[1] "Remove cluster labels:" "LACTB MUTATED"         
clus
  LACTB MUTATED LACTB WILD-TYPE 
              2             130 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-2J-AAB9      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-2J-AABH      TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-2J-AABU      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-2L-AAQI      TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I5 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-3A-A9I7      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-3A-A9IH      TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-6879 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-F2-A44G      TCGA-F2-A44H      TCGA-F2-A7TX      TCGA-F2-A8YN 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A545      TCGA-FB-A5VM 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-7919 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-7922      TCGA-HZ-7925      TCGA-HZ-7926      TCGA-HZ-8001 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-8002      TCGA-HZ-8003      TCGA-HZ-8005      TCGA-HZ-8315 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-8317      TCGA-HZ-8519      TCGA-HZ-8636      TCGA-HZ-8637 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A49G      TCGA-HZ-A49H      TCGA-HZ-A49I      TCGA-HZ-A4BH 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A4BK      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A77Q 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7646 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-7647      TCGA-IB-7652      TCGA-IB-7886      TCGA-IB-7887 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7891      TCGA-IB-7893 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-7897      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-OE-A75W      TCGA-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-US-A776      TCGA-US-A779 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-US-A77E      TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XD-AAUL      TCGA-YB-A89D      TCGA-YH-A8SY 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" 
D140V14, binary
                 cls
clus                0   1
  LACTB MUTATED     0   2
  LACTB WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      0    2
  LACTB WILD-TYPE    3  102
                        clus
vv                       LACTB MUTATED LACTB WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(141) Variable = TEKT4 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2              0  1
  TEKT4 MUTATED    3  3
  TEKT4 WILD-TYPE 59 69
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             128 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              3              69 
$`TEKT4 MUTATED`
TCGA-2J-AABR TCGA-3E-AAAZ TCGA-FB-A78T TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7888 
       14.40        71.74        12.43         1.08        19.82        43.79 

$`TEKT4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        22.26        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        12.39        75.12        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       24.07        14.76         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 
       15.35        23.80        41.33         4.04         3.62        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  TEKT4 MUTATED TEKT4 WILD-TYPE 
           1.08            0.13 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
          71.74           75.12 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
          17.11           13.50 
[1] "1.1 - 71.7 (17.1)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.9"
D141V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TEKT4 MUTATED          0        0         3         3         0        0
  TEKT4 WILD-TYPE        4        6        17        96         4        3
D141V3, multiclass
           clus
vv          TEKT4 MUTATED TEKT4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             3              17
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TEKT4 MUTATED     0   0     6
  TEKT4 WILD-TYPE   5  13   112
D141V4, multiclass
       clus
vv      TEKT4 MUTATED TEKT4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             6             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V5, binary
                 cls
clus                0   1
  TEKT4 MUTATED     3   3
  TEKT4 WILD-TYPE  29 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      3    3
  TEKT4 WILD-TYPE   29  101
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             3              29
  1             3             101
[1] 2 2
[1] FALSE
D141V6, binary
                 cls
clus               0  1
  TEKT4 MUTATED    4  0
  TEKT4 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      4    0
  TEKT4 WILD-TYPE   58    3
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             4              58
  1             0               3
[1] 2 2
[1] FALSE
D141V7, binary
                 cls
clus               0  1
  TEKT4 MUTATED    5  1
  TEKT4 WILD-TYPE 57 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      5    1
  TEKT4 WILD-TYPE   57   73
        clus
vv       TEKT4 MUTATED TEKT4 WILD-TYPE
  FEMALE             5              57
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEKT4 MUTATED                                     5
  TEKT4 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEKT4 MUTATED                                       1
  TEKT4 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEKT4 MUTATED                                                  0
  TEKT4 WILD-TYPE                                                2
D141V8, multiclass
                                                  clus
vv                                                 TEKT4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TEKT4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V9, continuous
D141V10, continuous
                 vv
clus              R0 R1 R2 RX
  TEKT4 MUTATED    5  0  0  0
  TEKT4 WILD-TYPE 72 48  1  3
D141V11, multiclass
    clus
vv   TEKT4 MUTATED TEKT4 WILD-TYPE
  R0             5              72
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEKT4 MUTATED       0                         1     5
  TEKT4 WILD-TYPE     2                         4   120
D141V13, multiclass
                           clus
vv                          TEKT4 MUTATED TEKT4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V14, binary
                 cls
clus                0   1
  TEKT4 MUTATED     1   4
  TEKT4 WILD-TYPE   2 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      1    4
  TEKT4 WILD-TYPE    2  100
                        clus
vv                       TEKT4 MUTATED TEKT4 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(142) Variable = MC3R MUTATION ANALYSIS
D142V1, survival
                sevent
clus2             0  1
  MC3R MUTATED    1  3
  MC3R WILD-TYPE 61 69
  MC3R MUTATED MC3R WILD-TYPE 
             4            130 
  MC3R MUTATED MC3R WILD-TYPE 
             3             69 
$`MC3R MUTATED`
TCGA-IB-7651 TCGA-IB-7890 TCGA-US-A77G TCGA-YH-A8SY 
       19.82        19.66         0.39        12.76 

$`MC3R WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 
       41.33         4.04         3.62        43.79        15.81        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       27.75        16.80        14.14        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        66.28         0.69 

  MC3R MUTATED MC3R WILD-TYPE 
          0.39           0.13 
  MC3R MUTATED MC3R WILD-TYPE 
         19.82          75.12 
  MC3R MUTATED MC3R WILD-TYPE 
        16.210         13.745 
[1] "0.4 - 19.8 (16.2)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.7"
D142V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MC3R MUTATED          0        1         0         2         1        0
  MC3R WILD-TYPE        4        5        20        97         3        3
D142V3, multiclass
           clus
vv          MC3R MUTATED MC3R WILD-TYPE
  STAGE IA             0              4
  STAGE IB             1              5
  STAGE IIA            0             20
  STAGE IIB            2             97
  STAGE III            1              3
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  MC3R MUTATED     0   1     3
  MC3R WILD-TYPE   5  12   115
D142V4, multiclass
       clus
vv      MC3R MUTATED MC3R WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V5, binary
                cls
clus               0   1
  MC3R MUTATED     1   3
  MC3R WILD-TYPE  31 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      1    3
  MC3R WILD-TYPE   31  101
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0            1             31
  1            3            101
[1] 2 2
[1] FALSE
D142V6, binary
                cls
clus              0  1
  MC3R MUTATED    2  0
  MC3R WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      2    0
  MC3R WILD-TYPE   60    3
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D142V7, binary
                cls
clus              0  1
  MC3R MUTATED    2  2
  MC3R WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      2    2
  MC3R WILD-TYPE   60   72
        clus
vv       MC3R MUTATED MC3R WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MC3R MUTATED                                     3
  MC3R WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MC3R MUTATED                                       0
  MC3R WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MC3R MUTATED                                                  0
  MC3R WILD-TYPE                                                2
D142V8, multiclass
                                                  clus
vv                                                 MC3R MUTATED MC3R WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V9, continuous
[1] "Remove cluster labels:" "MC3R MUTATED"          
clus
  MC3R MUTATED MC3R WILD-TYPE 
             1             47 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-YY-A8LH 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
D142V10, continuous
[1] "Remove cluster labels:" "MC3R MUTATED"          
clus
  MC3R MUTATED MC3R WILD-TYPE 
             1             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MC3R MUTATED    3  0  0  0
  MC3R WILD-TYPE 74 48  1  3
D142V11, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  R0            3             74
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MC3R MUTATED       0                         0     3
  MC3R WILD-TYPE     2                         5   122
D142V13, multiclass
                           clus
vv                          MC3R MUTATED MC3R WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V14, binary
                cls
clus               0   1
  MC3R MUTATED     0   3
  MC3R WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      0    3
  MC3R WILD-TYPE    3  101
                        clus
vv                       MC3R MUTATED MC3R WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(143) Variable = CSRNP3 MUTATION ANALYSIS
D143V1, survival
                  sevent
clus2               0  1
  CSRNP3 MUTATED    1  2
  CSRNP3 WILD-TYPE 61 70
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               3              131 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               70 
$`CSRNP3 MUTATED`
TCGA-FB-A4P6 TCGA-IB-7645 TCGA-IB-7651 
       11.93        49.38        19.82 

$`CSRNP3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           11.93             0.13 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           49.38            75.12 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           19.82            13.68 
[1] "11.9 - 49.4 (19.8)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "1.4"
D143V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CSRNP3 MUTATED          0        0         0         4         0        0
  CSRNP3 WILD-TYPE        4        6        20        95         4        3
D143V3, multiclass
           clus
vv          CSRNP3 MUTATED CSRNP3 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CSRNP3 MUTATED     0   0     4
  CSRNP3 WILD-TYPE   5  13   114
D143V4, multiclass
       clus
vv      CSRNP3 MUTATED CSRNP3 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V5, binary
                  cls
clus                 0   1
  CSRNP3 MUTATED     0   4
  CSRNP3 WILD-TYPE  32 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      0    4
  CSRNP3 WILD-TYPE   32  100
   clus
vv  CSRNP3 MUTATED CSRNP3 WILD-TYPE
  0              0               32
  1              4              100
[1] 2 2
[1] FALSE
D143V6, binary
                  cls
clus                0  1
  CSRNP3 MUTATED    2  0
  CSRNP3 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      2    0
  CSRNP3 WILD-TYPE   60    3
   clus
vv  CSRNP3 MUTATED CSRNP3 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D143V7, binary
                  cls
clus                0  1
  CSRNP3 MUTATED    3  1
  CSRNP3 WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      3    1
  CSRNP3 WILD-TYPE   59   73
        clus
vv       CSRNP3 MUTATED CSRNP3 WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CSRNP3 MUTATED                                     4
  CSRNP3 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CSRNP3 MUTATED                                       0
  CSRNP3 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CSRNP3 MUTATED                                                  0
  CSRNP3 WILD-TYPE                                                2
D143V8, multiclass
                                                  clus
vv                                                 CSRNP3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CSRNP3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V9, continuous
[1] "Remove cluster labels:" "CSRNP3 MUTATED"        
clus
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
D143V10, continuous
[1] "Remove cluster labels:" "CSRNP3 MUTATED"        
clus
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A5VM 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-YY-A8LH 
"CSRNP3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CSRNP3 MUTATED    3  0  0  0
  CSRNP3 WILD-TYPE 74 48  1  3
D143V11, multiclass
    clus
vv   CSRNP3 MUTATED CSRNP3 WILD-TYPE
  R0              3               74
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSRNP3 MUTATED       0                         0     3
  CSRNP3 WILD-TYPE     2                         5   122
D143V13, multiclass
                           clus
vv                          CSRNP3 MUTATED CSRNP3 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V14, binary
                  cls
clus                 0   1
  CSRNP3 MUTATED     1   2
  CSRNP3 WILD-TYPE   2 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      1    2
  CSRNP3 WILD-TYPE    2  102
                        clus
vv                       CSRNP3 MUTATED CSRNP3 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(144) Variable = PHF15 MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2              0  1
  PHF15 MUTATED    2  2
  PHF15 WILD-TYPE 60 70
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             130 
  PHF15 MUTATED PHF15 WILD-TYPE 
              2              70 
$`PHF15 MUTATED`
TCGA-IB-7651 TCGA-IB-A5ST TCGA-IB-A6UF TCGA-S4-A8RP 
       19.82        20.88        21.90        23.08 

$`PHF15 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        15.12         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        9.40        21.24        17.26        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  PHF15 MUTATED PHF15 WILD-TYPE 
          19.82            0.13 
  PHF15 MUTATED PHF15 WILD-TYPE 
          23.08           75.12 
  PHF15 MUTATED PHF15 WILD-TYPE 
         21.390          13.155 
[1] "19.8 - 23.1 (21.4)" "0.1 - 75.1 (13.2)" 
[1] "hr=" "1.9"
D144V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PHF15 MUTATED          0        0         0         4         0        0
  PHF15 WILD-TYPE        4        6        20        95         4        3
D144V3, multiclass
           clus
vv          PHF15 MUTATED PHF15 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PHF15 MUTATED     0   0     4
  PHF15 WILD-TYPE   5  13   114
D144V4, multiclass
       clus
vv      PHF15 MUTATED PHF15 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V5, binary
                 cls
clus                0   1
  PHF15 MUTATED     0   4
  PHF15 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      0    4
  PHF15 WILD-TYPE   32  100
   clus
vv  PHF15 MUTATED PHF15 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D144V6, binary
                 cls
clus               0  1
  PHF15 MUTATED    3  0
  PHF15 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      3    0
  PHF15 WILD-TYPE   59    3
   clus
vv  PHF15 MUTATED PHF15 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D144V7, binary
                 cls
clus               0  1
  PHF15 MUTATED    3  1
  PHF15 WILD-TYPE 59 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      3    1
  PHF15 WILD-TYPE   59   73
        clus
vv       PHF15 MUTATED PHF15 WILD-TYPE
  FEMALE             3              59
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF15 MUTATED                                     4
  PHF15 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF15 MUTATED                                       0
  PHF15 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF15 MUTATED                                                  0
  PHF15 WILD-TYPE                                                2
D144V8, multiclass
                                                  clus
vv                                                 PHF15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PHF15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V9, continuous
D144V10, continuous
[1] "Remove cluster labels:" "PHF15 MUTATED"         
clus
  PHF15 MUTATED PHF15 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
     TCGA-YY-A8LH 
"PHF15 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PHF15 MUTATED    3  1  0  0
  PHF15 WILD-TYPE 74 47  1  3
D144V11, multiclass
    clus
vv   PHF15 MUTATED PHF15 WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF15 MUTATED       0                         0     4
  PHF15 WILD-TYPE     2                         5   121
D144V13, multiclass
                           clus
vv                          PHF15 MUTATED PHF15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V14, binary
                 cls
clus                0   1
  PHF15 MUTATED     0   3
  PHF15 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      0    3
  PHF15 WILD-TYPE    3  101
                        clus
vv                       PHF15 MUTATED PHF15 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(145) Variable = ZBTB4 MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2              0  1
  ZBTB4 MUTATED    0  3
  ZBTB4 WILD-TYPE 62 69
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              3             131 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              3              69 
$`ZBTB4 MUTATED`
TCGA-HZ-8636 TCGA-IB-7651 TCGA-US-A77E 
       17.92        19.82        14.14 

$`ZBTB4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       12.43        14.93        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       27.75        16.80         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
          14.14            0.13 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
          19.82           75.12 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
          17.92           13.32 
[1] "14.1 - 19.8 (17.9)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.7"
D145V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZBTB4 MUTATED          0        0         0         2         0        1
  ZBTB4 WILD-TYPE        4        6        20        97         4        2
D145V3, multiclass
           clus
vv          ZBTB4 MUTATED ZBTB4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             2              97
  STAGE III             0               4
  STAGE IV              1               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ZBTB4 MUTATED     0   0     3
  ZBTB4 WILD-TYPE   5  13   115
D145V4, multiclass
       clus
vv      ZBTB4 MUTATED ZBTB4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V5, binary
                 cls
clus                0   1
  ZBTB4 MUTATED     1   2
  ZBTB4 WILD-TYPE  31 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      1    2
  ZBTB4 WILD-TYPE   31  102
   clus
vv  ZBTB4 MUTATED ZBTB4 WILD-TYPE
  0             1              31
  1             2             102
[1] 2 2
[1] FALSE
D145V6, binary
                 cls
clus               0  1
  ZBTB4 MUTATED    1  1
  ZBTB4 WILD-TYPE 61  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      1    1
  ZBTB4 WILD-TYPE   61    2
   clus
vv  ZBTB4 MUTATED ZBTB4 WILD-TYPE
  0             1              61
  1             1               2
[1] 2 2
[1] FALSE
D145V7, binary
                 cls
clus               0  1
  ZBTB4 MUTATED    2  1
  ZBTB4 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      2    1
  ZBTB4 WILD-TYPE   60   73
        clus
vv       ZBTB4 MUTATED ZBTB4 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZBTB4 MUTATED                                     2
  ZBTB4 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZBTB4 MUTATED                                       1
  ZBTB4 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZBTB4 MUTATED                                                  0
  ZBTB4 WILD-TYPE                                                2
D145V8, multiclass
                                                  clus
vv                                                 ZBTB4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZBTB4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V9, continuous
[1] "Remove cluster labels:" "ZBTB4 MUTATED"         
clus
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
D145V10, continuous
[1] "Remove cluster labels:" "ZBTB4 MUTATED"         
clus
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZBTB4 MUTATED    1  2  0  0
  ZBTB4 WILD-TYPE 76 46  1  3
D145V11, multiclass
    clus
vv   ZBTB4 MUTATED ZBTB4 WILD-TYPE
  R0             1              76
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB4 MUTATED       0                         0     3
  ZBTB4 WILD-TYPE     2                         5   122
D145V13, multiclass
                           clus
vv                          ZBTB4 MUTATED ZBTB4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V14, binary
                 cls
clus                0   1
  ZBTB4 MUTATED     0   3
  ZBTB4 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      0    3
  ZBTB4 WILD-TYPE    3  101
                        clus
vv                       ZBTB4 MUTATED ZBTB4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(146) Variable = RSPO1 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2              0  1
  RSPO1 MUTATED    1  2
  RSPO1 WILD-TYPE 61 70
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             131 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              70 
$`RSPO1 MUTATED`
TCGA-F2-6879 TCGA-FB-AAPS TCGA-IB-7651 
       10.98         7.50        19.82 

$`RSPO1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       71.74         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  RSPO1 MUTATED RSPO1 WILD-TYPE 
           7.50            0.13 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
          19.82           75.12 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
          10.98           13.81 
[1] "7.5 - 19.8 (11.0)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.7"
D146V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RSPO1 MUTATED          0        0         0         3         0        0
  RSPO1 WILD-TYPE        4        6        20        96         4        3
D146V3, multiclass
           clus
vv          RSPO1 MUTATED RSPO1 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RSPO1 MUTATED     0   1     2
  RSPO1 WILD-TYPE   5  12   116
D146V4, multiclass
       clus
vv      RSPO1 MUTATED RSPO1 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             2             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V5, binary
                 cls
clus                0   1
  RSPO1 MUTATED     0   3
  RSPO1 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      0    3
  RSPO1 WILD-TYPE   32  101
   clus
vv  RSPO1 MUTATED RSPO1 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D146V6, binary
                 cls
clus               0  1
  RSPO1 MUTATED    2  0
  RSPO1 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      2    0
  RSPO1 WILD-TYPE   60    3
   clus
vv  RSPO1 MUTATED RSPO1 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D146V7, binary
                 cls
clus               0  1
  RSPO1 MUTATED    2  1
  RSPO1 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      2    1
  RSPO1 WILD-TYPE   60   73
        clus
vv       RSPO1 MUTATED RSPO1 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RSPO1 MUTATED                                     2
  RSPO1 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RSPO1 MUTATED                                       1
  RSPO1 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RSPO1 MUTATED                                                  0
  RSPO1 WILD-TYPE                                                2
D146V8, multiclass
                                                  clus
vv                                                 RSPO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RSPO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V9, continuous
[1] "Remove cluster labels:" "RSPO1 MUTATED"         
clus
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
D146V10, continuous
[1] "Remove cluster labels:" "RSPO1 MUTATED"         
clus
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPY      TCGA-H6-8124 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-YY-A8LH 
"RSPO1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RSPO1 MUTATED    3  0  0  0
  RSPO1 WILD-TYPE 74 48  1  3
D146V11, multiclass
    clus
vv   RSPO1 MUTATED RSPO1 WILD-TYPE
  R0             3              74
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RSPO1 MUTATED       0                         0     3
  RSPO1 WILD-TYPE     2                         5   122
D146V13, multiclass
                           clus
vv                          RSPO1 MUTATED RSPO1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V14, binary
                 cls
clus                0   1
  RSPO1 MUTATED     0   2
  RSPO1 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      0    2
  RSPO1 WILD-TYPE    3  102
                        clus
vv                       RSPO1 MUTATED RSPO1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(147) Variable = WWP2 MUTATION ANALYSIS
D147V1, survival
                sevent
clus2             0  1
  WWP2 MUTATED    2  2
  WWP2 WILD-TYPE 60 70
  WWP2 MUTATED WWP2 WILD-TYPE 
             4            130 
  WWP2 MUTATED WWP2 WILD-TYPE 
             2             70 
$`WWP2 MUTATED`
TCGA-HZ-A49G TCGA-HZ-A77P TCGA-IB-AAUO TCGA-US-A77E 
       21.70        10.85         7.86        14.14 

$`WWP2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       12.43        14.93        17.92        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
       21.60         5.26         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       16.80         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  WWP2 MUTATED WWP2 WILD-TYPE 
          7.86           0.13 
  WWP2 MUTATED WWP2 WILD-TYPE 
         21.70          75.12 
  WWP2 MUTATED WWP2 WILD-TYPE 
        12.495         13.745 
[1] "7.9 - 21.7 (12.5)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D147V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WWP2 MUTATED          0        0         0         5         0        0
  WWP2 WILD-TYPE        4        6        20        94         4        3
D147V3, multiclass
           clus
vv          WWP2 MUTATED WWP2 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  WWP2 MUTATED     0   1     4
  WWP2 WILD-TYPE   5  12   114
D147V4, multiclass
       clus
vv      WWP2 MUTATED WWP2 WILD-TYPE
  T1               0              5
  T2               1             12
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V5, binary
                cls
clus              0  1
  WWP2 MUTATED    0  5
  WWP2 WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      0    5
  WWP2 WILD-TYPE   32   99
   clus
vv  WWP2 MUTATED WWP2 WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D147V6, binary
                cls
clus              0  1
  WWP2 MUTATED    1  0
  WWP2 WILD-TYPE 61  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      1    0
  WWP2 WILD-TYPE   61    3
   clus
vv  WWP2 MUTATED WWP2 WILD-TYPE
  0            1             61
  1            0              3
[1] 2 2
[1] FALSE
D147V7, binary
                cls
clus              0  1
  WWP2 MUTATED    3  2
  WWP2 WILD-TYPE 59 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      3    2
  WWP2 WILD-TYPE   59   72
        clus
vv       WWP2 MUTATED WWP2 WILD-TYPE
  FEMALE            3             59
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WWP2 MUTATED                                     3
  WWP2 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WWP2 MUTATED                                       2
  WWP2 WILD-TYPE                                     9
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WWP2 MUTATED                                                  0
  WWP2 WILD-TYPE                                                2
D147V8, multiclass
                                                  clus
vv                                                 WWP2 MUTATED WWP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V9, continuous
D147V10, continuous
                vv
clus             R0 R1 R2 RX
  WWP2 MUTATED    2  3  0  0
  WWP2 WILD-TYPE 75 45  1  3
D147V11, multiclass
    clus
vv   WWP2 MUTATED WWP2 WILD-TYPE
  R0            2             75
  R1            3             45
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WWP2 MUTATED       0                         0     5
  WWP2 WILD-TYPE     2                         5   120
D147V13, multiclass
                           clus
vv                          WWP2 MUTATED WWP2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V14, binary
                cls
clus               0   1
  WWP2 MUTATED     1   4
  WWP2 WILD-TYPE   2 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      1    4
  WWP2 WILD-TYPE    2  100
                        clus
vv                       WWP2 MUTATED WWP2 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(148) Variable = CPNE2 MUTATION ANALYSIS
D148V1, survival
                 sevent
clus2              0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 61 70
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             131 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2              70 
$`CPNE2 MUTATED`
TCGA-3A-A9I5 TCGA-3E-AAAZ TCGA-IB-7651 
       53.00        71.74        19.82 

$`CPNE2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        12.39        75.12        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CPNE2 MUTATED CPNE2 WILD-TYPE 
          19.82            0.13 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
          71.74           75.12 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
          53.00           13.32 
[1] "19.8 - 71.7 (53.0)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "2.7"
D148V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CPNE2 MUTATED          1        0         1         1         0        0
  CPNE2 WILD-TYPE        3        6        19        98         4        3
D148V3, multiclass
           clus
vv          CPNE2 MUTATED CPNE2 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             1              98
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CPNE2 MUTATED     1   0     2
  CPNE2 WILD-TYPE   4  13   116
D148V4, multiclass
       clus
vv      CPNE2 MUTATED CPNE2 WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4             2             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V5, binary
                 cls
clus                0   1
  CPNE2 MUTATED     2   1
  CPNE2 WILD-TYPE  30 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      2    1
  CPNE2 WILD-TYPE   30  103
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             2              30
  1             1             103
[1] 2 2
[1] FALSE
D148V6, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  0
  CPNE2 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    0
  CPNE2 WILD-TYPE   61    3
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D148V7, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE   61   72
        clus
vv       CPNE2 MUTATED CPNE2 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CPNE2 MUTATED                                     3
  CPNE2 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CPNE2 MUTATED                                       0
  CPNE2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CPNE2 MUTATED                                                  0
  CPNE2 WILD-TYPE                                                2
D148V8, multiclass
                                                  clus
vv                                                 CPNE2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CPNE2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V9, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D148V10, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CPNE2 MUTATED    2  0  0  0
  CPNE2 WILD-TYPE 75 48  1  3
D148V11, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             127 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AAB9      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABH      TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABU      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQI      TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I7 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-6879      TCGA-F2-A44G      TCGA-F2-A44H      TCGA-F2-A7TX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A4P5      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY      TCGA-FB-AAPZ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-7919      TCGA-HZ-7922      TCGA-HZ-7925 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7645      TCGA-IB-7646      TCGA-IB-7647 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-7886 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7890 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-7893      TCGA-IB-7897      TCGA-IB-8126 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-M8-A5N4      TCGA-OE-A75W 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP      TCGA-US-A774 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E      TCGA-US-A77G 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XD-AAUL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D148V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPNE2 MUTATED       0                         0     3
  CPNE2 WILD-TYPE     2                         5   122
D148V13, multiclass
                           clus
vv                          CPNE2 MUTATED CPNE2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V14, binary
                 cls
clus                0   1
  CPNE2 MUTATED     1   2
  CPNE2 WILD-TYPE   2 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE    2  102
                        clus
vv                       CPNE2 MUTATED CPNE2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(149) Variable = WDR36 MUTATION ANALYSIS
D149V1, survival
                 sevent
clus2              0  1
  WDR36 MUTATED    0  3
  WDR36 WILD-TYPE 62 69
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             131 
  WDR36 MUTATED WDR36 WILD-TYPE 
              3              69 
$`WDR36 MUTATED`
TCGA-2J-AAB9 TCGA-HZ-7925 TCGA-IB-7649 
       20.61        20.19        15.35 

$`WDR36 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        19.82        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  WDR36 MUTATED WDR36 WILD-TYPE 
          15.35            0.13 
  WDR36 MUTATED WDR36 WILD-TYPE 
          20.61           75.12 
  WDR36 MUTATED WDR36 WILD-TYPE 
          20.19           13.32 
[1] "15.3 - 20.6 (20.2)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.5"
D149V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WDR36 MUTATED          0        0         0         3         0        0
  WDR36 WILD-TYPE        4        6        20        96         4        3
D149V3, multiclass
           clus
vv          WDR36 MUTATED WDR36 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  WDR36 MUTATED     0   0     3
  WDR36 WILD-TYPE   5  13   115
D149V4, multiclass
       clus
vv      WDR36 MUTATED WDR36 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V5, binary
                 cls
clus                0   1
  WDR36 MUTATED     0   3
  WDR36 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      0    3
  WDR36 WILD-TYPE   32  101
   clus
vv  WDR36 MUTATED WDR36 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D149V6, binary
                 cls
clus               0  1
  WDR36 MUTATED    2  0
  WDR36 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      2    0
  WDR36 WILD-TYPE   60    3
   clus
vv  WDR36 MUTATED WDR36 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D149V7, binary
                 cls
clus               0  1
  WDR36 MUTATED    2  1
  WDR36 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      2    1
  WDR36 WILD-TYPE   60   73
        clus
vv       WDR36 MUTATED WDR36 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDR36 MUTATED                                     3
  WDR36 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDR36 MUTATED                                       0
  WDR36 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDR36 MUTATED                                                  0
  WDR36 WILD-TYPE                                                2
D149V8, multiclass
                                                  clus
vv                                                 WDR36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 WDR36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V9, continuous
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
D149V10, continuous
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  WDR36 MUTATED    2  1  0  0
  WDR36 WILD-TYPE 75 47  1  3
D149V11, multiclass
    clus
vv   WDR36 MUTATED WDR36 WILD-TYPE
  R0             2              75
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR36 MUTATED       0                         0     2
  WDR36 WILD-TYPE     2                         5   123
D149V13, multiclass
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              2             130 
     TCGA-2J-AAB1      TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABR      TCGA-2J-AABU 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-3A-A9I5      TCGA-3A-A9I7 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-3A-A9IU      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-6879      TCGA-F2-A44G 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-F2-A44H      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A545      TCGA-FB-A5VM      TCGA-FB-A78T 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPY      TCGA-FB-AAPZ 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-7919      TCGA-HZ-7922 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7646      TCGA-IB-7647      TCGA-IB-7651 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7888      TCGA-IB-7889      TCGA-IB-7891      TCGA-IB-7893 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-7897      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-US-A776      TCGA-US-A779 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-US-A77E      TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XD-AAUL      TCGA-YB-A89D      TCGA-YH-A8SY 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
D149V14, binary
                 cls
clus                0   1
  WDR36 MUTATED     0   1
  WDR36 WILD-TYPE   3 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      0    1
  WDR36 WILD-TYPE    3  103
                        clus
vv                       WDR36 MUTATED WDR36 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             1             103
[1] 2 2
[1] FALSE

Clustering(150) Variable = CYTH4 MUTATION ANALYSIS
D150V1, survival
                 sevent
clus2              0  1
  CYTH4 MUTATED    0  3
  CYTH4 WILD-TYPE 62 69
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             131 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3              69 
$`CYTH4 MUTATED`
TCGA-HZ-7926 TCGA-IB-7887 TCGA-US-A77G 
       17.03         3.62         0.39 

$`CYTH4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         4.04        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       27.75        16.80        14.14        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CYTH4 MUTATED CYTH4 WILD-TYPE 
           0.39            0.13 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
          17.03           75.12 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
           3.62           13.81 
[1] "0.4 - 17.0 (3.6)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "4.6"
D150V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CYTH4 MUTATED          0        0         0         3         0        0
  CYTH4 WILD-TYPE        4        6        20        96         4        3
D150V3, multiclass
           clus
vv          CYTH4 MUTATED CYTH4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CYTH4 MUTATED     0   0     3
  CYTH4 WILD-TYPE   5  13   115
D150V4, multiclass
       clus
vv      CYTH4 MUTATED CYTH4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V5, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   3
  CYTH4 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    3
  CYTH4 WILD-TYPE   32  101
   clus
vv  CYTH4 MUTATED CYTH4 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D150V6, binary
                 cls
clus               0  1
  CYTH4 MUTATED    1  0
  CYTH4 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      1    0
  CYTH4 WILD-TYPE   61    3
   clus
vv  CYTH4 MUTATED CYTH4 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D150V7, binary
                 cls
clus               0  1
  CYTH4 MUTATED    1  2
  CYTH4 WILD-TYPE 61 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      1    2
  CYTH4 WILD-TYPE   61   72
        clus
vv       CYTH4 MUTATED CYTH4 WILD-TYPE
  FEMALE             1              61
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CYTH4 MUTATED                                     3
  CYTH4 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CYTH4 MUTATED                                       0
  CYTH4 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CYTH4 MUTATED                                                  0
  CYTH4 WILD-TYPE                                                2
D150V8, multiclass
                                                  clus
vv                                                 CYTH4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CYTH4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V9, continuous
[1] "Remove cluster labels:" "CYTH4 MUTATED"         
clus
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
D150V10, continuous
                 vv
clus              R0 R1 R2 RX
  CYTH4 MUTATED    1  1  0  1
  CYTH4 WILD-TYPE 76 47  1  2
D150V11, multiclass
    clus
vv   CYTH4 MUTATED CYTH4 WILD-TYPE
  R0             1              76
  R1             1              47
  R2             0               1
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYTH4 MUTATED       0                         1     2
  CYTH4 WILD-TYPE     2                         4   123
D150V13, multiclass
                           clus
vv                          CYTH4 MUTATED CYTH4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V14, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   3
  CYTH4 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    3
  CYTH4 WILD-TYPE    3  101
                        clus
vv                       CYTH4 MUTATED CYTH4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(151) Variable = BOC MUTATION ANALYSIS
D151V1, survival
               sevent
clus2            0  1
  BOC MUTATED    1  3
  BOC WILD-TYPE 61 69
  BOC MUTATED BOC WILD-TYPE 
            4           130 
  BOC MUTATED BOC WILD-TYPE 
            3            69 
$`BOC MUTATED`
TCGA-3A-A9IC TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-XD-AAUI 
       24.26         0.23        19.82        12.03 

$`BOC WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84         7.36        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 
       21.60         5.26        10.85         1.08        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL 
       16.80        14.14         0.39        13.81        12.99        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  BOC MUTATED BOC WILD-TYPE 
         0.23          0.13 
  BOC MUTATED BOC WILD-TYPE 
        24.26         75.12 
  BOC MUTATED BOC WILD-TYPE 
       15.925        13.745 
[1] "0.2 - 24.3 (15.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.3"
D151V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BOC MUTATED          0        1         0         3         0        0
  BOC WILD-TYPE        4        5        20        96         4        3
D151V3, multiclass
           clus
vv          BOC MUTATED BOC WILD-TYPE
  STAGE IA            0             4
  STAGE IB            1             5
  STAGE IIA           0            20
  STAGE IIB           3            96
  STAGE III           0             4
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  BOC MUTATED     0   1     3
  BOC WILD-TYPE   5  12   115
D151V4, multiclass
       clus
vv      BOC MUTATED BOC WILD-TYPE
  T1              0             5
  T2              1            12
  T3+T4           3           115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V5, binary
               cls
clus              0   1
  BOC MUTATED     1   3
  BOC WILD-TYPE  31 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      1    3
  BOC WILD-TYPE   31  101
   clus
vv  BOC MUTATED BOC WILD-TYPE
  0           1            31
  1           3           101
[1] 2 2
[1] FALSE
D151V6, binary
               cls
clus             0  1
  BOC MUTATED    1  0
  BOC WILD-TYPE 61  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      1    0
  BOC WILD-TYPE   61    3
   clus
vv  BOC MUTATED BOC WILD-TYPE
  0           1            61
  1           0             3
[1] 2 2
[1] FALSE
D151V7, binary
               cls
clus             0  1
  BOC MUTATED    3  1
  BOC WILD-TYPE 59 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      3    1
  BOC WILD-TYPE   59   73
        clus
vv       BOC MUTATED BOC WILD-TYPE
  FEMALE           3            59
  MALE             1            73
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BOC MUTATED                                     4
  BOC WILD-TYPE                                 118
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BOC MUTATED                                       0
  BOC WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BOC MUTATED                                                  0
  BOC WILD-TYPE                                                2
D151V8, multiclass
                                                  clus
vv                                                 BOC MUTATED BOC WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V9, continuous
[1] "Remove cluster labels:" "BOC MUTATED"           
clus
  BOC MUTATED BOC WILD-TYPE 
            2            46 
   TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-FB-A78T    TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-H6-A45N 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-7644    TCGA-IB-7649    TCGA-IB-7885 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891    TCGA-IB-8126    TCGA-IB-8127 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU    TCGA-LB-A7SX    TCGA-LB-A9Q5 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP    TCGA-US-A774    TCGA-XD-AAUL 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-YY-A8LH 
"BOC WILD-TYPE" 
D151V10, continuous
               vv
clus            R0 R1 R2 RX
  BOC MUTATED    3  1  0  0
  BOC WILD-TYPE 74 47  1  3
D151V11, multiclass
    clus
vv   BOC MUTATED BOC WILD-TYPE
  R0           3            74
  R1           1            47
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BOC MUTATED       0                         0     4
  BOC WILD-TYPE     2                         5   121
D151V13, multiclass
                           clus
vv                          BOC MUTATED BOC WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V14, binary
               cls
clus              0   1
  BOC MUTATED     0   4
  BOC WILD-TYPE   3 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      0    4
  BOC WILD-TYPE    3  100
                        clus
vv                       BOC MUTATED BOC WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4           100
[1] 2 2
[1] FALSE

Clustering(152) Variable = C5ORF51 MUTATION ANALYSIS
D152V1, survival
                   sevent
clus2                0  1
  C5ORF51 MUTATED    1  2
  C5ORF51 WILD-TYPE 61 70
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               131 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                70 
$`C5ORF51 MUTATED`
TCGA-HZ-8005 TCGA-IB-7651 TCGA-IB-7885 
        3.95        19.82        41.33 

$`C5ORF51 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 
       49.38         4.77        21.90        15.35        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
             3.95              0.13 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
            41.33             75.12 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
            19.82             13.68 
[1] "4.0 - 41.3 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D152V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C5ORF51 MUTATED          0        0         0         3         0        0
  C5ORF51 WILD-TYPE        4        6        20        96         4        3
D152V3, multiclass
           clus
vv          C5ORF51 MUTATED C5ORF51 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               3                96
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  C5ORF51 MUTATED     0   0     3
  C5ORF51 WILD-TYPE   5  13   115
D152V4, multiclass
       clus
vv      C5ORF51 MUTATED C5ORF51 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V5, binary
                   cls
clus                  0   1
  C5ORF51 MUTATED     0   3
  C5ORF51 WILD-TYPE  32 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      0    3
  C5ORF51 WILD-TYPE   32  101
   clus
vv  C5ORF51 MUTATED C5ORF51 WILD-TYPE
  0               0                32
  1               3               101
[1] 2 2
[1] FALSE
D152V6, binary
                   cls
clus                 0  1
  C5ORF51 MUTATED    2  0
  C5ORF51 WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      2    0
  C5ORF51 WILD-TYPE   60    3
   clus
vv  C5ORF51 MUTATED C5ORF51 WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D152V7, binary
                   cls
clus                 0  1
  C5ORF51 MUTATED    2  1
  C5ORF51 WILD-TYPE 60 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      2    1
  C5ORF51 WILD-TYPE   60   73
        clus
vv       C5ORF51 MUTATED C5ORF51 WILD-TYPE
  FEMALE               2                60
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C5ORF51 MUTATED                                     3
  C5ORF51 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C5ORF51 MUTATED                                       0
  C5ORF51 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C5ORF51 MUTATED                                                  0
  C5ORF51 WILD-TYPE                                                2
D152V8, multiclass
                                                  clus
vv                                                 C5ORF51 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 C5ORF51 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V9, continuous
[1] "Remove cluster labels:" "C5ORF51 MUTATED"       
clus
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
D152V10, continuous
[1] "Remove cluster labels:" "C5ORF51 MUTATED"       
clus
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                37 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7886        TCGA-IB-7891 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-YY-A8LH 
"C5ORF51 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  C5ORF51 MUTATED    2  1  0  0
  C5ORF51 WILD-TYPE 75 47  1  3
D152V11, multiclass
    clus
vv   C5ORF51 MUTATED C5ORF51 WILD-TYPE
  R0               2                75
  R1               1                47
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C5ORF51 MUTATED       0                         0     3
  C5ORF51 WILD-TYPE     2                         5   122
D152V13, multiclass
                           clus
vv                          C5ORF51 MUTATED C5ORF51 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V14, binary
                   cls
clus                  0   1
  C5ORF51 MUTATED     0   3
  C5ORF51 WILD-TYPE   3 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      0    3
  C5ORF51 WILD-TYPE    3  101
                        clus
vv                       C5ORF51 MUTATED C5ORF51 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               101
[1] 2 2
[1] FALSE

Clustering(153) Variable = LILRB2 MUTATION ANALYSIS
D153V1, survival
                  sevent
clus2               0  1
  LILRB2 MUTATED    0  4
  LILRB2 WILD-TYPE 62 68
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              130 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4               68 
$`LILRB2 MUTATED`
TCGA-HZ-8317 TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-A5SQ 
       12.43        19.82        43.79         7.20 

$`LILRB2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04         3.62        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
       15.98         2.47        17.16        12.00        15.85        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  LILRB2 MUTATED LILRB2 WILD-TYPE 
            7.20             0.13 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
           43.79            75.12 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
          16.125           13.745 
[1] "7.2 - 43.8 (16.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.5"
D153V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LILRB2 MUTATED          0        1         1         2         0        0
  LILRB2 WILD-TYPE        4        5        19        97         4        3
D153V3, multiclass
           clus
vv          LILRB2 MUTATED LILRB2 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               1                5
  STAGE IIA              1               19
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  LILRB2 MUTATED     0   1     3
  LILRB2 WILD-TYPE   5  12   115
D153V4, multiclass
       clus
vv      LILRB2 MUTATED LILRB2 WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V5, binary
                  cls
clus                 0   1
  LILRB2 MUTATED     2   2
  LILRB2 WILD-TYPE  30 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      2    2
  LILRB2 WILD-TYPE   30  102
   clus
vv  LILRB2 MUTATED LILRB2 WILD-TYPE
  0              2               30
  1              2              102
[1] 2 2
[1] FALSE
D153V6, binary
                  cls
clus                0  1
  LILRB2 MUTATED    3  0
  LILRB2 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      3    0
  LILRB2 WILD-TYPE   59    3
   clus
vv  LILRB2 MUTATED LILRB2 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D153V7, binary
                  cls
clus                0  1
  LILRB2 MUTATED    4  0
  LILRB2 WILD-TYPE 58 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      4    0
  LILRB2 WILD-TYPE   58   74
        clus
vv       LILRB2 MUTATED LILRB2 WILD-TYPE
  FEMALE              4               58
  MALE                0               74
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LILRB2 MUTATED                                     4
  LILRB2 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LILRB2 MUTATED                                       0
  LILRB2 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LILRB2 MUTATED                                                  0
  LILRB2 WILD-TYPE                                                2
D153V8, multiclass
                                                  clus
vv                                                 LILRB2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 LILRB2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V9, continuous
[1] "Remove cluster labels:" "LILRB2 MUTATED"        
clus
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
D153V10, continuous
[1] "Remove cluster labels:" "LILRB2 MUTATED"        
clus
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LILRB2 MUTATED    3  1  0  0
  LILRB2 WILD-TYPE 74 47  1  3
D153V11, multiclass
    clus
vv   LILRB2 MUTATED LILRB2 WILD-TYPE
  R0              3               74
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LILRB2 MUTATED       0                         1     3
  LILRB2 WILD-TYPE     2                         4   122
D153V13, multiclass
                           clus
vv                          LILRB2 MUTATED LILRB2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V14, binary
                  cls
clus                 0   1
  LILRB2 MUTATED     0   4
  LILRB2 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      0    4
  LILRB2 WILD-TYPE    3  100
                        clus
vv                       LILRB2 MUTATED LILRB2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(154) Variable = FLVCR1 MUTATION ANALYSIS
D154V1, survival
                  sevent
clus2               0  1
  FLVCR1 MUTATED    1  2
  FLVCR1 WILD-TYPE 61 70
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              131 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               70 
$`FLVCR1 MUTATED`
TCGA-3A-A9IU TCGA-HZ-A77Q TCGA-IB-7651 
       15.06         1.08        19.82 

$`FLVCR1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
       21.60         5.26        10.85         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
            1.08             0.13 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           19.82            75.12 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           15.06            13.68 
[1] "1.1 - 19.8 (15.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.7"
D154V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FLVCR1 MUTATED          0        0         0         3         0        0
  FLVCR1 WILD-TYPE        4        6        20        96         4        3
D154V3, multiclass
           clus
vv          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  FLVCR1 MUTATED     0   0     3
  FLVCR1 WILD-TYPE   5  13   115
D154V4, multiclass
       clus
vv      FLVCR1 MUTATED FLVCR1 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V5, binary
                  cls
clus                 0   1
  FLVCR1 MUTATED     0   3
  FLVCR1 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE   32  101
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D154V6, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    1  0
  FLVCR1 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      1    0
  FLVCR1 WILD-TYPE   61    3
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D154V7, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    2  1
  FLVCR1 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      2    1
  FLVCR1 WILD-TYPE   60   73
        clus
vv       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FLVCR1 MUTATED                                     2
  FLVCR1 WILD-TYPE                                 120
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FLVCR1 MUTATED                                       1
  FLVCR1 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FLVCR1 MUTATED                                                  0
  FLVCR1 WILD-TYPE                                                2
D154V8, multiclass
                                                  clus
vv                                                 FLVCR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 FLVCR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V9, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
D154V10, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  FLVCR1 MUTATED    3  0  0  0
  FLVCR1 WILD-TYPE 74 48  1  3
D154V11, multiclass
    clus
vv   FLVCR1 MUTATED FLVCR1 WILD-TYPE
  R0              3               74
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLVCR1 MUTATED       0                         0     3
  FLVCR1 WILD-TYPE     2                         5   122
D154V13, multiclass
                           clus
vv                          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V14, binary
                  cls
clus                 0   1
  FLVCR1 MUTATED     0   3
  FLVCR1 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE    3  101
                        clus
vv                       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(155) Variable = ZNF483 MUTATION ANALYSIS
D155V1, survival
                  sevent
clus2               0  1
  ZNF483 MUTATED    2  2
  ZNF483 WILD-TYPE 60 70
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              130 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               2               70 
$`ZNF483 MUTATED`
TCGA-2J-AAB4 TCGA-FB-A78T TCGA-HZ-8315 TCGA-IB-7887 
       23.97        12.43         9.83         3.62 

$`ZNF483 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         3.95        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        23.80        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  ZNF483 MUTATED ZNF483 WILD-TYPE 
            3.62             0.13 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
           23.97            75.12 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
          11.130           13.825 
[1] "3.6 - 24.0 (11.1)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.1"
D155V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF483 MUTATED          0        0         1         3         0        0
  ZNF483 WILD-TYPE        4        6        19        96         4        3
D155V3, multiclass
           clus
vv          ZNF483 MUTATED ZNF483 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF483 MUTATED     0   1     3
  ZNF483 WILD-TYPE   5  12   115
D155V4, multiclass
       clus
vv      ZNF483 MUTATED ZNF483 WILD-TYPE
  T1                 0                5
  T2                 1               12
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V5, binary
                  cls
clus                 0   1
  ZNF483 MUTATED     1   3
  ZNF483 WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      1    3
  ZNF483 WILD-TYPE   31  101
   clus
vv  ZNF483 MUTATED ZNF483 WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D155V6, binary
                  cls
clus                0  1
  ZNF483 MUTATED    3  0
  ZNF483 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      3    0
  ZNF483 WILD-TYPE   59    3
   clus
vv  ZNF483 MUTATED ZNF483 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D155V7, binary
                  cls
clus                0  1
  ZNF483 MUTATED    3  1
  ZNF483 WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      3    1
  ZNF483 WILD-TYPE   59   73
        clus
vv       ZNF483 MUTATED ZNF483 WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF483 MUTATED                                     3
  ZNF483 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF483 MUTATED                                       1
  ZNF483 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF483 MUTATED                                                  0
  ZNF483 WILD-TYPE                                                2
D155V8, multiclass
                                                  clus
vv                                                 ZNF483 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF483 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V9, continuous
[1] "Remove cluster labels:" "ZNF483 MUTATED"        
clus
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-AAPS 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
D155V10, continuous
[1] "Remove cluster labels:" "ZNF483 MUTATED"        
clus
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF483 MUTATED    2  2  0  0
  ZNF483 WILD-TYPE 75 46  1  3
D155V11, multiclass
    clus
vv   ZNF483 MUTATED ZNF483 WILD-TYPE
  R0              2               75
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF483 MUTATED       0                         0     4
  ZNF483 WILD-TYPE     2                         5   121
D155V13, multiclass
                           clus
vv                          ZNF483 MUTATED ZNF483 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V14, binary
                  cls
clus                 0   1
  ZNF483 MUTATED     0   3
  ZNF483 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      0    3
  ZNF483 WILD-TYPE    3  101
                        clus
vv                       ZNF483 MUTATED ZNF483 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(156) Variable = NDUFV2 MUTATION ANALYSIS
D156V1, survival
                  sevent
clus2               0  1
  NDUFV2 MUTATED    3  0
  NDUFV2 WILD-TYPE 59 72
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              131 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               0               72 
$`NDUFV2 MUTATED`
TCGA-F2-A8YN TCGA-S4-A8RO TCGA-YY-A8LH 
       17.00        17.26        66.28 

$`NDUFV2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 
       71.74        10.98         7.66        19.27         3.12         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 
        3.12        15.32         9.40        21.24        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76         0.69 

  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           17.00             0.13 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           66.28            75.12 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           17.26            13.32 
[1] "17.0 - 66.3 (17.3)" "0.1 - 75.1 (13.3)" 
[1] "hr="     "2.7e+07"
D156V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NDUFV2 MUTATED          0        0         1         2         0        0
  NDUFV2 WILD-TYPE        4        6        19        97         4        3
D156V3, multiclass
           clus
vv          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  NDUFV2 MUTATED     0   0     3
  NDUFV2 WILD-TYPE   5  13   115
D156V4, multiclass
       clus
vv      NDUFV2 MUTATED NDUFV2 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V5, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     1   2
  NDUFV2 WILD-TYPE  31 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE   31  102
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               31
  1              2              102
[1] 2 2
[1] FALSE
D156V6, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  0
  NDUFV2 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    0
  NDUFV2 WILD-TYPE   61    3
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D156V7, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    2  1
  NDUFV2 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    1
  NDUFV2 WILD-TYPE   60   73
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NDUFV2 MUTATED                                     3
  NDUFV2 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NDUFV2 MUTATED                                       0
  NDUFV2 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NDUFV2 MUTATED                                                  0
  NDUFV2 WILD-TYPE                                                2
D156V8, multiclass
                                                  clus
vv                                                 NDUFV2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 NDUFV2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V9, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
D156V10, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7886       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XD-AAUL 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NDUFV2 MUTATED    1  2  0  0
  NDUFV2 WILD-TYPE 76 46  1  3
D156V11, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  R0              1               76
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NDUFV2 MUTATED       0                         0     3
  NDUFV2 WILD-TYPE     2                         5   122
D156V13, multiclass
                           clus
vv                          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V14, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     0   3
  NDUFV2 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      0    3
  NDUFV2 WILD-TYPE    3  101
                        clus
vv                       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(157) Variable = PSMB4 MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2              0  1
  PSMB4 MUTATED    2  2
  PSMB4 WILD-TYPE 60 70
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             130 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              2              70 
$`PSMB4 MUTATED`
TCGA-2J-AABA TCGA-IB-8127 TCGA-IB-A5SO TCGA-YY-A8LH 
       19.96        17.16        12.00        66.28 

$`PSMB4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ 
       21.30         3.85        15.98         2.47        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.32        11.51        12.76         0.69 

  PSMB4 MUTATED PSMB4 WILD-TYPE 
          12.00            0.13 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
          66.28           75.12 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
          18.56           13.50 
[1] "12.0 - 66.3 (18.6)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.8"
D157V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PSMB4 MUTATED          0        0         0         4         0        0
  PSMB4 WILD-TYPE        4        6        20        95         4        3
D157V3, multiclass
           clus
vv          PSMB4 MUTATED PSMB4 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PSMB4 MUTATED     0   0     4
  PSMB4 WILD-TYPE   5  13   114
D157V4, multiclass
       clus
vv      PSMB4 MUTATED PSMB4 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V5, binary
                 cls
clus                0   1
  PSMB4 MUTATED     0   4
  PSMB4 WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      0    4
  PSMB4 WILD-TYPE   32  100
   clus
vv  PSMB4 MUTATED PSMB4 WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D157V6, binary
                 cls
clus               0  1
  PSMB4 MUTATED    3  0
  PSMB4 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      3    0
  PSMB4 WILD-TYPE   59    3
   clus
vv  PSMB4 MUTATED PSMB4 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D157V7, binary
                 cls
clus               0  1
  PSMB4 MUTATED    1  3
  PSMB4 WILD-TYPE 61 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      1    3
  PSMB4 WILD-TYPE   61   71
        clus
vv       PSMB4 MUTATED PSMB4 WILD-TYPE
  FEMALE             1              61
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PSMB4 MUTATED                                     4
  PSMB4 WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PSMB4 MUTATED                                       0
  PSMB4 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PSMB4 MUTATED                                                  0
  PSMB4 WILD-TYPE                                                2
D157V8, multiclass
                                                  clus
vv                                                 PSMB4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PSMB4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V9, continuous
D157V10, continuous
[1] "Remove cluster labels:" "PSMB4 MUTATED"         
clus
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-A5SS 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-XD-AAUL 
"PSMB4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PSMB4 MUTATED    2  2  0  0
  PSMB4 WILD-TYPE 75 46  1  3
D157V11, multiclass
    clus
vv   PSMB4 MUTATED PSMB4 WILD-TYPE
  R0             2              75
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSMB4 MUTATED       0                         0     4
  PSMB4 WILD-TYPE     2                         5   121
D157V13, multiclass
                           clus
vv                          PSMB4 MUTATED PSMB4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V14, binary
                 cls
clus                0   1
  PSMB4 MUTATED     0   2
  PSMB4 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      0    2
  PSMB4 WILD-TYPE    3  102
                        clus
vv                       PSMB4 MUTATED PSMB4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(158) Variable = KIAA1045 MUTATION ANALYSIS
D158V1, survival
                    sevent
clus2                 0  1
  KIAA1045 MUTATED    2  3
  KIAA1045 WILD-TYPE 60 69
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
                 5                129 
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
                 3                 69 
$`KIAA1045 MUTATED`
TCGA-HZ-8002 TCGA-IB-7651 TCGA-IB-8126 TCGA-Q3-A5QY TCGA-XD-AAUI 
       12.03        19.82         2.47        13.68        12.03 

$`KIAA1045 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D 
       14.14         0.39        13.81        12.99        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
              2.47               0.13 
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
             19.82              75.12 
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
             12.03              13.84 
[1] "2.5 - 19.8 (12.0)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.7"
D158V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KIAA1045 MUTATED          0        0         0         4         1        0
  KIAA1045 WILD-TYPE        4        6        20        95         3        3
D158V3, multiclass
           clus
vv          KIAA1045 MUTATED KIAA1045 WILD-TYPE
  STAGE IA                 0                  4
  STAGE IB                 0                  6
  STAGE IIA                0                 20
  STAGE IIB                4                 95
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  KIAA1045 MUTATED     0   0     5
  KIAA1045 WILD-TYPE   5  13   113
D158V4, multiclass
       clus
vv      KIAA1045 MUTATED KIAA1045 WILD-TYPE
  T1                   0                  5
  T2                   0                 13
  T3+T4                5                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V5, binary
                    cls
clus                  0  1
  KIAA1045 MUTATED    0  5
  KIAA1045 WILD-TYPE 32 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1045 MUTATED      0    5
  KIAA1045 WILD-TYPE   32   99
   clus
vv  KIAA1045 MUTATED KIAA1045 WILD-TYPE
  0                0                 32
  1                5                 99
[1] 2 2
[1] FALSE
D158V6, binary
                    cls
clus                  0  1
  KIAA1045 MUTATED    2  0
  KIAA1045 WILD-TYPE 60  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1045 MUTATED      2    0
  KIAA1045 WILD-TYPE   60    3
   clus
vv  KIAA1045 MUTATED KIAA1045 WILD-TYPE
  0                2                 60
  1                0                  3
[1] 2 2
[1] FALSE
D158V7, binary
                    cls
clus                  0  1
  KIAA1045 MUTATED    3  2
  KIAA1045 WILD-TYPE 59 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1045 MUTATED      3    2
  KIAA1045 WILD-TYPE   59   72
        clus
vv       KIAA1045 MUTATED KIAA1045 WILD-TYPE
  FEMALE                3                 59
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA1045 MUTATED                                     5
  KIAA1045 WILD-TYPE                                 117
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA1045 MUTATED                                       0
  KIAA1045 WILD-TYPE                                    11
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA1045 MUTATED                                                  0
  KIAA1045 WILD-TYPE                                                2
D158V8, multiclass
                                                  clus
vv                                                 KIAA1045 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 KIAA1045 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V9, continuous
[1] "Remove cluster labels:" "KIAA1045 MUTATED"      
clus
  KIAA1045 MUTATED KIAA1045 WILD-TYPE 
                 2                 46 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A4P6         TCGA-FB-A5VM 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPS         TCGA-FB-AAPY 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-H6-8124         TCGA-H6-A45N         TCGA-HZ-A77Q 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7885         TCGA-IB-7886 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8127 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUU         TCGA-LB-A7SX 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" "KIAA1045 WILD-TYPE" 
        TCGA-YY-A8LH 
"KIAA1045 WILD-TYPE" 
D158V10, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA1045 MUTATED    3  2  0  0
  KIAA1045 WILD-TYPE 74 46  1  3
D158V11, multiclass
    clus
vv   KIAA1045 MUTATED KIAA1045 WILD-TYPE
  R0                3                 74
  R1                2                 46
  R2                0                  1
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1045 MUTATED       0                         0     5
  KIAA1045 WILD-TYPE     2                         5   120
D158V13, multiclass
                           clus
vv                          KIAA1045 MUTATED KIAA1045 WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V14, binary
                    cls
clus                  0  1
  KIAA1045 MUTATED    0  5
  KIAA1045 WILD-TYPE  3 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1045 MUTATED      0    5
  KIAA1045 WILD-TYPE    3   99
                        clus
vv                       KIAA1045 MUTATED KIAA1045 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                 99
[1] 2 2
[1] FALSE

Clustering(159) Variable = KLK15 MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2              0  1
  KLK15 MUTATED    2  3
  KLK15 WILD-TYPE 60 69
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             129 
  KLK15 MUTATED KLK15 WILD-TYPE 
              3              69 
$`KLK15 MUTATED`
TCGA-2J-AAB9 TCGA-3A-A9I5 TCGA-3A-A9J0 TCGA-IB-7651 TCGA-IB-A6UG 
       20.61        53.00        12.39        19.82         1.35 

$`KLK15 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       34.09        10.13        75.12        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
       19.27         3.12        17.00         5.88        11.93        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  KLK15 MUTATED KLK15 WILD-TYPE 
           1.35            0.13 
  KLK15 MUTATED KLK15 WILD-TYPE 
          53.00           75.12 
  KLK15 MUTATED KLK15 WILD-TYPE 
          19.82           13.68 
[1] "1.4 - 53.0 (19.8)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D159V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KLK15 MUTATED          1        0         0         4         0        0
  KLK15 WILD-TYPE        3        6        20        95         4        3
D159V3, multiclass
           clus
vv          KLK15 MUTATED KLK15 WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KLK15 MUTATED     1   0     4
  KLK15 WILD-TYPE   4  13   114
D159V4, multiclass
       clus
vv      KLK15 MUTATED KLK15 WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V5, binary
                 cls
clus                0   1
  KLK15 MUTATED     1   4
  KLK15 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      1    4
  KLK15 WILD-TYPE   31  100
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D159V6, binary
                 cls
clus               0  1
  KLK15 MUTATED    3  0
  KLK15 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      3    0
  KLK15 WILD-TYPE   59    3
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus               0  1
  KLK15 MUTATED    2  3
  KLK15 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      2    3
  KLK15 WILD-TYPE   60   71
        clus
vv       KLK15 MUTATED KLK15 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK15 MUTATED                                     5
  KLK15 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK15 MUTATED                                       0
  KLK15 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK15 MUTATED                                                  0
  KLK15 WILD-TYPE                                                2
D159V8, multiclass
                                                  clus
vv                                                 KLK15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KLK15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V9, continuous
[1] "Remove cluster labels:" "KLK15 MUTATED"         
clus
  KLK15 MUTATED KLK15 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
D159V10, continuous
[1] "Remove cluster labels:" "KLK15 MUTATED"         
clus
  KLK15 MUTATED KLK15 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-YY-A8LH 
"KLK15 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KLK15 MUTATED    4  1  0  0
  KLK15 WILD-TYPE 73 47  1  3
D159V11, multiclass
    clus
vv   KLK15 MUTATED KLK15 WILD-TYPE
  R0             4              73
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK15 MUTATED       0                         0     5
  KLK15 WILD-TYPE     2                         5   120
D159V13, multiclass
                           clus
vv                          KLK15 MUTATED KLK15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V14, binary
                 cls
clus                0   1
  KLK15 MUTATED     0   4
  KLK15 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      0    4
  KLK15 WILD-TYPE    3  100
                        clus
vv                       KLK15 MUTATED KLK15 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(160) Variable = ZNF660 MUTATION ANALYSIS
D160V1, survival
                  sevent
clus2               0  1
  ZNF660 MUTATED    1  2
  ZNF660 WILD-TYPE 61 70
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               3              131 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               2               70 
$`ZNF660 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7889 
       19.82        41.33        15.81 

$`ZNF660 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04         3.62        43.79        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  ZNF660 MUTATED ZNF660 WILD-TYPE 
           15.81             0.13 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
           41.33            75.12 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
           19.82            13.32 
[1] "15.8 - 41.3 (19.8)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.4"
D160V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF660 MUTATED          0        0         0         3         0        0
  ZNF660 WILD-TYPE        4        6        20        96         4        3
D160V3, multiclass
           clus
vv          ZNF660 MUTATED ZNF660 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF660 MUTATED     0   0     3
  ZNF660 WILD-TYPE   5  13   115
D160V4, multiclass
       clus
vv      ZNF660 MUTATED ZNF660 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V5, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     0   3
  ZNF660 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      0    3
  ZNF660 WILD-TYPE   32  101
   clus
vv  ZNF660 MUTATED ZNF660 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D160V6, binary
                  cls
clus                0  1
  ZNF660 MUTATED    3  0
  ZNF660 WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      3    0
  ZNF660 WILD-TYPE   59    3
   clus
vv  ZNF660 MUTATED ZNF660 WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D160V7, binary
                  cls
clus                0  1
  ZNF660 MUTATED    3  0
  ZNF660 WILD-TYPE 59 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      3    0
  ZNF660 WILD-TYPE   59   74
        clus
vv       ZNF660 MUTATED ZNF660 WILD-TYPE
  FEMALE              3               59
  MALE                0               74
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF660 MUTATED                                     3
  ZNF660 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF660 MUTATED                                       0
  ZNF660 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF660 MUTATED                                                  0
  ZNF660 WILD-TYPE                                                2
D160V8, multiclass
                                                  clus
vv                                                 ZNF660 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF660 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V9, continuous
[1] "Remove cluster labels:" "ZNF660 MUTATED"        
clus
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
D160V10, continuous
[1] "Remove cluster labels:" "ZNF660 MUTATED"        
clus
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7886       TCGA-IB-7891 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" "ZNF660 WILD-TYPE" 
      TCGA-YY-A8LH 
"ZNF660 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF660 MUTATED    3  0  0  0
  ZNF660 WILD-TYPE 74 48  1  3
D160V11, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  R0              3               74
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF660 MUTATED       0                         0     3
  ZNF660 WILD-TYPE     2                         5   122
D160V13, multiclass
                           clus
vv                          ZNF660 MUTATED ZNF660 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V14, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     0   3
  ZNF660 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      0    3
  ZNF660 WILD-TYPE    3  101
                        clus
vv                       ZNF660 MUTATED ZNF660 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(161) Variable = CCDC87 MUTATION ANALYSIS
D161V1, survival
                  sevent
clus2               0  1
  CCDC87 MUTATED    2  1
  CCDC87 WILD-TYPE 60 71
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              131 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               1               71 
$`CCDC87 MUTATED`
TCGA-FB-A4P5 TCGA-IB-A7M4 TCGA-Q3-AA2A 
        5.88        15.88         3.12 

$`CCDC87 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 
       10.29        19.20         8.78        15.45        13.68        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  CCDC87 MUTATED CCDC87 WILD-TYPE 
            3.12             0.13 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
           15.88            75.12 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
            5.88            13.81 
[1] "3.1 - 15.9 (5.9)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "1.4"
D161V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CCDC87 MUTATED          0        1         0         2         0        0
  CCDC87 WILD-TYPE        4        5        20        97         4        3
D161V3, multiclass
           clus
vv          CCDC87 MUTATED CCDC87 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               1                5
  STAGE IIA              0               20
  STAGE IIB              2               97
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CCDC87 MUTATED     0   0     3
  CCDC87 WILD-TYPE   5  13   115
D161V4, multiclass
       clus
vv      CCDC87 MUTATED CCDC87 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V5, binary
                  cls
clus                 0   1
  CCDC87 MUTATED     0   3
  CCDC87 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    3
  CCDC87 WILD-TYPE   32  101
   clus
vv  CCDC87 MUTATED CCDC87 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D161V6, binary
                  cls
clus                0  1
  CCDC87 MUTATED    0  0
  CCDC87 WILD-TYPE 62  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    0
  CCDC87 WILD-TYPE   62    3
D161V7, binary
                  cls
clus                0  1
  CCDC87 MUTATED    2  1
  CCDC87 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      2    1
  CCDC87 WILD-TYPE   60   73
        clus
vv       CCDC87 MUTATED CCDC87 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC87 MUTATED                                     3
  CCDC87 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC87 MUTATED                                       0
  CCDC87 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC87 MUTATED                                                  0
  CCDC87 WILD-TYPE                                                2
D161V8, multiclass
                                                  clus
vv                                                 CCDC87 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CCDC87 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V9, continuous
[1] "Remove cluster labels:" "CCDC87 MUTATED"        
clus
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
D161V10, continuous
[1] "Remove cluster labels:" "CCDC87 MUTATED"        
clus
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P6       TCGA-FB-A5VM 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-YY-A8LH 
"CCDC87 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CCDC87 MUTATED    2  0  0  1
  CCDC87 WILD-TYPE 75 48  1  2
D161V11, multiclass
    clus
vv   CCDC87 MUTATED CCDC87 WILD-TYPE
  R0              2               75
  R1              0               48
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC87 MUTATED       0                         0     3
  CCDC87 WILD-TYPE     2                         5   122
D161V13, multiclass
                           clus
vv                          CCDC87 MUTATED CCDC87 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V14, binary
                  cls
clus                 0   1
  CCDC87 MUTATED     0   3
  CCDC87 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    3
  CCDC87 WILD-TYPE    3  101
                        clus
vv                       CCDC87 MUTATED CCDC87 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(162) Variable = KIF4B MUTATION ANALYSIS
D162V1, survival
                 sevent
clus2              0  1
  KIF4B MUTATED    2  2
  KIF4B WILD-TYPE 60 70
  KIF4B MUTATED KIF4B WILD-TYPE 
              4             130 
  KIF4B MUTATED KIF4B WILD-TYPE 
              2              70 
$`KIF4B MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A6UG TCGA-RB-AA9M 
       19.82        41.33         1.35         9.40 

$`KIF4B WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        15.12        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  KIF4B MUTATED KIF4B WILD-TYPE 
           1.35            0.13 
  KIF4B MUTATED KIF4B WILD-TYPE 
          41.33           75.12 
  KIF4B MUTATED KIF4B WILD-TYPE 
         14.610          13.745 
[1] "1.4 - 41.3 (14.6)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D162V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KIF4B MUTATED          0        0         0         4         0        0
  KIF4B WILD-TYPE        4        6        20        95         4        3
D162V3, multiclass
           clus
vv          KIF4B MUTATED KIF4B WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KIF4B MUTATED     1   0     3
  KIF4B WILD-TYPE   4  13   115
D162V4, multiclass
       clus
vv      KIF4B MUTATED KIF4B WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V5, binary
                 cls
clus                0   1
  KIF4B MUTATED     0   4
  KIF4B WILD-TYPE  32 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      0    4
  KIF4B WILD-TYPE   32  100
   clus
vv  KIF4B MUTATED KIF4B WILD-TYPE
  0             0              32
  1             4             100
[1] 2 2
[1] FALSE
D162V6, binary
                 cls
clus               0  1
  KIF4B MUTATED    3  0
  KIF4B WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      3    0
  KIF4B WILD-TYPE   59    3
   clus
vv  KIF4B MUTATED KIF4B WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D162V7, binary
                 cls
clus               0  1
  KIF4B MUTATED    2  2
  KIF4B WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      2    2
  KIF4B WILD-TYPE   60   72
        clus
vv       KIF4B MUTATED KIF4B WILD-TYPE
  FEMALE             2              60
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIF4B MUTATED                                     4
  KIF4B WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIF4B MUTATED                                       0
  KIF4B WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIF4B MUTATED                                                  0
  KIF4B WILD-TYPE                                                2
D162V8, multiclass
                                                  clus
vv                                                 KIF4B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KIF4B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V9, continuous
D162V10, continuous
                 vv
clus              R0 R1 R2 RX
  KIF4B MUTATED    3  1  0  0
  KIF4B WILD-TYPE 74 47  1  3
D162V11, multiclass
    clus
vv   KIF4B MUTATED KIF4B WILD-TYPE
  R0             3              74
  R1             1              47
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF4B MUTATED       0                         0     4
  KIF4B WILD-TYPE     2                         5   121
D162V13, multiclass
                           clus
vv                          KIF4B MUTATED KIF4B WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V14, binary
                 cls
clus                0   1
  KIF4B MUTATED     0   4
  KIF4B WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      0    4
  KIF4B WILD-TYPE    3  100
                        clus
vv                       KIF4B MUTATED KIF4B WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(163) Variable = ENPP7 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2              0  1
  ENPP7 MUTATED    0  5
  ENPP7 WILD-TYPE 62 67
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             129 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5              67 
$`ENPP7 MUTATED`
TCGA-2J-AAB1 TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-AAUO TCGA-US-A77E 
        2.17        71.74        19.82         7.86        14.14 

$`ENPP7 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        12.39        75.12        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  ENPP7 MUTATED ENPP7 WILD-TYPE 
           2.17            0.13 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          71.74           75.12 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          14.14           13.68 
[1] "2.2 - 71.7 (14.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D163V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ENPP7 MUTATED          0        0         1         4         0        0
  ENPP7 WILD-TYPE        4        6        19        95         4        3
D163V3, multiclass
           clus
vv          ENPP7 MUTATED ENPP7 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ENPP7 MUTATED     0   0     5
  ENPP7 WILD-TYPE   5  13   113
D163V4, multiclass
       clus
vv      ENPP7 MUTATED ENPP7 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V5, binary
                 cls
clus                0   1
  ENPP7 MUTATED     1   4
  ENPP7 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      1    4
  ENPP7 WILD-TYPE   31  100
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             1              31
  1             4             100
[1] 2 2
[1] FALSE
D163V6, binary
                 cls
clus               0  1
  ENPP7 MUTATED    3  0
  ENPP7 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      3    0
  ENPP7 WILD-TYPE   59    3
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D163V7, binary
                 cls
clus               0  1
  ENPP7 MUTATED    2  3
  ENPP7 WILD-TYPE 60 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      2    3
  ENPP7 WILD-TYPE   60   71
        clus
vv       ENPP7 MUTATED ENPP7 WILD-TYPE
  FEMALE             2              60
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ENPP7 MUTATED                                     3
  ENPP7 WILD-TYPE                                 119
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ENPP7 MUTATED                                       2
  ENPP7 WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ENPP7 MUTATED                                                  0
  ENPP7 WILD-TYPE                                                2
D163V8, multiclass
                                                  clus
vv                                                 ENPP7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ENPP7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V9, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              46 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
D163V10, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              37 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ENPP7 MUTATED    2  2  0  0
  ENPP7 WILD-TYPE 75 46  1  3
D163V11, multiclass
    clus
vv   ENPP7 MUTATED ENPP7 WILD-TYPE
  R0             2              75
  R1             2              46
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENPP7 MUTATED       0                         0     5
  ENPP7 WILD-TYPE     2                         5   120
D163V13, multiclass
                           clus
vv                          ENPP7 MUTATED ENPP7 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V14, binary
                 cls
clus                0   1
  ENPP7 MUTATED     1   3
  ENPP7 WILD-TYPE   2 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      1    3
  ENPP7 WILD-TYPE    2  101
                        clus
vv                       ENPP7 MUTATED ENPP7 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(164) Variable = TNRC6C MUTATION ANALYSIS
D164V1, survival
                  sevent
clus2               0  1
  TNRC6C MUTATED    3  3
  TNRC6C WILD-TYPE 59 69
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              128 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               3               69 
$`TNRC6C MUTATED`
TCGA-2J-AABR TCGA-FB-A78T TCGA-FB-AAPU TCGA-HZ-8317 TCGA-IB-7651 TCGA-RB-AA9M 
       14.40        12.43        12.53        12.43        19.82         9.40 

$`TNRC6C WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        22.26        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.93        24.07        14.76         7.50        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       15.55         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
        0.69         3.95         9.83        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
            9.40             0.13 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           19.82            75.12 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
          12.480           13.825 
[1] "9.4 - 19.8 (12.5)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.2"
D164V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TNRC6C MUTATED          0        0         2         4         0        0
  TNRC6C WILD-TYPE        4        6        18        95         4        3
D164V3, multiclass
           clus
vv          TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              2               18
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TNRC6C MUTATED     1   0     5
  TNRC6C WILD-TYPE   4  13   113
D164V4, multiclass
       clus
vv      TNRC6C MUTATED TNRC6C WILD-TYPE
  T1                 1                4
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V5, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     2   4
  TNRC6C WILD-TYPE  30 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      2    4
  TNRC6C WILD-TYPE   30  100
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              2               30
  1              4              100
[1] 2 2
[1] FALSE
D164V6, binary
                  cls
clus                0  1
  TNRC6C MUTATED    3  0
  TNRC6C WILD-TYPE 59  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      3    0
  TNRC6C WILD-TYPE   59    3
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              3               59
  1              0                3
[1] 2 2
[1] FALSE
D164V7, binary
                  cls
clus                0  1
  TNRC6C MUTATED    5  1
  TNRC6C WILD-TYPE 57 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      5    1
  TNRC6C WILD-TYPE   57   73
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE              5               57
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNRC6C MUTATED                                     6
  TNRC6C WILD-TYPE                                 116
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNRC6C MUTATED                                       0
  TNRC6C WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNRC6C MUTATED                                                  0
  TNRC6C WILD-TYPE                                                2
D164V8, multiclass
                                                  clus
vv                                                 TNRC6C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TNRC6C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V9, continuous
[1] "Remove cluster labels:" "TNRC6C MUTATED"        
clus
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-AAPS 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
D164V10, continuous
[1] "Remove cluster labels:" "TNRC6C MUTATED"        
clus
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-YY-A8LH 
"TNRC6C WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TNRC6C MUTATED    4  2  0  0
  TNRC6C WILD-TYPE 73 46  1  3
D164V11, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0              4               73
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNRC6C MUTATED       1                         0     5
  TNRC6C WILD-TYPE     1                         5   120
D164V13, multiclass
                           clus
vv                          TNRC6C MUTATED TNRC6C WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V14, binary
                  cls
clus                0  1
  TNRC6C MUTATED    0  5
  TNRC6C WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      0    5
  TNRC6C WILD-TYPE    3   99
                        clus
vv                       TNRC6C MUTATED TNRC6C WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(165) Variable = NAA40 MUTATION ANALYSIS
D165V1, survival
                 sevent
clus2              0  1
  NAA40 MUTATED    1  2
  NAA40 WILD-TYPE 61 70
  NAA40 MUTATED NAA40 WILD-TYPE 
              3             131 
  NAA40 MUTATED NAA40 WILD-TYPE 
              2              70 
$`NAA40 MUTATED`
TCGA-HZ-A49H TCGA-IB-7651 TCGA-RB-A7B8 
       16.14        19.82        15.32 

$`NAA40 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH 
       12.43        14.93        17.92        21.70        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  NAA40 MUTATED NAA40 WILD-TYPE 
          15.32            0.13 
  NAA40 MUTATED NAA40 WILD-TYPE 
          19.82           75.12 
  NAA40 MUTATED NAA40 WILD-TYPE 
          16.14           13.32 
[1] "15.3 - 19.8 (16.1)" "0.1 - 75.1 (13.3)" 
[1] "hr=" "1.1"
D165V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NAA40 MUTATED          0        0         0         3         0        0
  NAA40 WILD-TYPE        4        6        20        96         4        3
D165V3, multiclass
           clus
vv          NAA40 MUTATED NAA40 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  NAA40 MUTATED     0   0     3
  NAA40 WILD-TYPE   5  13   115
D165V4, multiclass
       clus
vv      NAA40 MUTATED NAA40 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V5, binary
                 cls
clus                0   1
  NAA40 MUTATED     0   3
  NAA40 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA40 MUTATED      0    3
  NAA40 WILD-TYPE   32  101
   clus
vv  NAA40 MUTATED NAA40 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D165V6, binary
                 cls
clus               0  1
  NAA40 MUTATED    1  0
  NAA40 WILD-TYPE 61  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA40 MUTATED      1    0
  NAA40 WILD-TYPE   61    3
   clus
vv  NAA40 MUTATED NAA40 WILD-TYPE
  0             1              61
  1             0               3
[1] 2 2
[1] FALSE
D165V7, binary
                 cls
clus               0  1
  NAA40 MUTATED    3  0
  NAA40 WILD-TYPE 59 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA40 MUTATED      3    0
  NAA40 WILD-TYPE   59   74
        clus
vv       NAA40 MUTATED NAA40 WILD-TYPE
  FEMALE             3              59
  MALE               0              74
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAA40 MUTATED                                     2
  NAA40 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAA40 MUTATED                                       1
  NAA40 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAA40 MUTATED                                                  0
  NAA40 WILD-TYPE                                                2
D165V8, multiclass
                                                  clus
vv                                                 NAA40 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NAA40 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V9, continuous
[1] "Remove cluster labels:" "NAA40 MUTATED"         
clus
  NAA40 MUTATED NAA40 WILD-TYPE 
              1              47 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
D165V10, continuous
[1] "Remove cluster labels:" "NAA40 MUTATED"         
clus
  NAA40 MUTATED NAA40 WILD-TYPE 
              1              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"NAA40 WILD-TYPE" "NAA40 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NAA40 MUTATED    3  0  0  0
  NAA40 WILD-TYPE 74 48  1  3
D165V11, multiclass
    clus
vv   NAA40 MUTATED NAA40 WILD-TYPE
  R0             3              74
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA40 MUTATED       0                         0     3
  NAA40 WILD-TYPE     2                         5   122
D165V13, multiclass
                           clus
vv                          NAA40 MUTATED NAA40 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V14, binary
                 cls
clus                0   1
  NAA40 MUTATED     0   3
  NAA40 WILD-TYPE   3 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA40 MUTATED      0    3
  NAA40 WILD-TYPE    3  101
                        clus
vv                       NAA40 MUTATED NAA40 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             101
[1] 2 2
[1] FALSE

Clustering(166) Variable = AKAP13 MUTATION ANALYSIS
D166V1, survival
                  sevent
clus2               0  1
  AKAP13 MUTATED    1  5
  AKAP13 WILD-TYPE 61 67
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               6              128 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               5               67 
$`AKAP13 MUTATED`
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8636 TCGA-HZ-A77Q TCGA-IB-7649 TCGA-IB-7651 
       17.03        12.03        17.92         1.08        15.35        19.82 

$`AKAP13 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  AKAP13 MUTATED AKAP13 WILD-TYPE 
            1.08             0.13 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           19.82            75.12 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           16.19            13.50 
[1] "1.1 - 19.8 (16.2)" "0.1 - 75.1 (13.5)"
[1] "hr=" "1.8"
D166V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AKAP13 MUTATED          0        0         0         5         0        1
  AKAP13 WILD-TYPE        4        6        20        94         4        2
D166V3, multiclass
           clus
vv          AKAP13 MUTATED AKAP13 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              5               94
  STAGE III              0                4
  STAGE IV               1                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  AKAP13 MUTATED     0   0     6
  AKAP13 WILD-TYPE   5  13   112
D166V4, multiclass
       clus
vv      AKAP13 MUTATED AKAP13 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              6              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V5, binary
                  cls
clus                0  1
  AKAP13 MUTATED    1  5
  AKAP13 WILD-TYPE 31 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      1    5
  AKAP13 WILD-TYPE   31   99
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0              1               31
  1              5               99
[1] 2 2
[1] FALSE
D166V6, binary
                  cls
clus                0  1
  AKAP13 MUTATED    2  1
  AKAP13 WILD-TYPE 60  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      2    1
  AKAP13 WILD-TYPE   60    2
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0              2               60
  1              1                2
[1] 2 2
[1] FALSE
D166V7, binary
                  cls
clus                0  1
  AKAP13 MUTATED    4  2
  AKAP13 WILD-TYPE 58 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      4    2
  AKAP13 WILD-TYPE   58   72
        clus
vv       AKAP13 MUTATED AKAP13 WILD-TYPE
  FEMALE              4               58
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AKAP13 MUTATED                                     5
  AKAP13 WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AKAP13 MUTATED                                       1
  AKAP13 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AKAP13 MUTATED                                                  0
  AKAP13 WILD-TYPE                                                2
D166V8, multiclass
                                                  clus
vv                                                 AKAP13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 AKAP13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V9, continuous
D166V10, continuous
                  vv
clus               R0 R1 R2 RX
  AKAP13 MUTATED    3  2  0  1
  AKAP13 WILD-TYPE 74 46  1  2
D166V11, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  R0              3               74
  R1              2               46
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKAP13 MUTATED       0                         1     4
  AKAP13 WILD-TYPE     2                         4   121
D166V13, multiclass
                           clus
vv                          AKAP13 MUTATED AKAP13 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V14, binary
                  cls
clus                0  1
  AKAP13 MUTATED    0  5
  AKAP13 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      0    5
  AKAP13 WILD-TYPE    3   99
                        clus
vv                       AKAP13 MUTATED AKAP13 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(167) Variable = ASH1L MUTATION ANALYSIS
D167V1, survival
                 sevent
clus2              0  1
  ASH1L MUTATED    4  2
  ASH1L WILD-TYPE 58 70
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             128 
  ASH1L MUTATED ASH1L WILD-TYPE 
              2              70 
$`ASH1L MUTATED`
TCGA-3A-A9IH TCGA-HZ-7925 TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7885 TCGA-YB-A89D 
       28.73        20.19         1.08        19.82        41.33        11.51 

$`ASH1L WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        15.35        23.80         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY 
        0.39        13.81        12.99        12.03        13.32        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  ASH1L MUTATED ASH1L WILD-TYPE 
           1.08            0.13 
  ASH1L MUTATED ASH1L WILD-TYPE 
          41.33           75.12 
  ASH1L MUTATED ASH1L WILD-TYPE 
         20.005          13.500 
[1] "1.1 - 41.3 (20.0)" "0.1 - 75.1 (13.5)"
[1] "hr=" "2.3"
D167V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ASH1L MUTATED          1        0         0         5         0        0
  ASH1L WILD-TYPE        3        6        20        94         4        3
D167V3, multiclass
           clus
vv          ASH1L MUTATED ASH1L WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             5              94
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ASH1L MUTATED     1   0     5
  ASH1L WILD-TYPE   4  13   113
D167V4, multiclass
       clus
vv      ASH1L MUTATED ASH1L WILD-TYPE
  T1                1               4
  T2                0              13
  T3+T4             5             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V5, binary
                 cls
clus               0  1
  ASH1L MUTATED    1  5
  ASH1L WILD-TYPE 31 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      1    5
  ASH1L WILD-TYPE   31   99
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             1              31
  1             5              99
[1] 2 2
[1] FALSE
D167V6, binary
                 cls
clus               0  1
  ASH1L MUTATED    2  0
  ASH1L WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      2    0
  ASH1L WILD-TYPE   60    3
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D167V7, binary
                 cls
clus               0  1
  ASH1L MUTATED    4  2
  ASH1L WILD-TYPE 58 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      4    2
  ASH1L WILD-TYPE   58   72
        clus
vv       ASH1L MUTATED ASH1L WILD-TYPE
  FEMALE             4              58
  MALE               2              72
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASH1L MUTATED                                     5
  ASH1L WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASH1L MUTATED                                       1
  ASH1L WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASH1L MUTATED                                                  0
  ASH1L WILD-TYPE                                                2
D167V8, multiclass
                                                  clus
vv                                                 ASH1L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ASH1L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V9, continuous
D167V10, continuous
                 vv
clus              R0 R1 R2 RX
  ASH1L MUTATED    6  0  0  0
  ASH1L WILD-TYPE 71 48  1  3
D167V11, multiclass
    clus
vv   ASH1L MUTATED ASH1L WILD-TYPE
  R0             6              71
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASH1L MUTATED       0                         0     6
  ASH1L WILD-TYPE     2                         5   119
D167V13, multiclass
                           clus
vv                          ASH1L MUTATED ASH1L WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V14, binary
                 cls
clus               0  1
  ASH1L MUTATED    0  6
  ASH1L WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      0    6
  ASH1L WILD-TYPE    3   98
                        clus
vv                       ASH1L MUTATED ASH1L WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(168) Variable = ATP2C2 MUTATION ANALYSIS
D168V1, survival
                  sevent
clus2               0  1
  ATP2C2 MUTATED    2  2
  ATP2C2 WILD-TYPE 60 70
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              130 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               70 
$`ATP2C2 MUTATED`
TCGA-3A-A9IH TCGA-FB-AAPS TCGA-IB-7651 TCGA-US-A77G 
       28.73         7.50        19.82         0.39 

$`ATP2C2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       16.80        14.14        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
            0.39             0.13 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
           28.73            75.12 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
          13.660           13.745 
[1] "0.4 - 28.7 (13.7)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.1"
D168V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ATP2C2 MUTATED          1        0         0         3         0        0
  ATP2C2 WILD-TYPE        3        6        20        96         4        3
D168V3, multiclass
           clus
vv          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  STAGE IA               1                3
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP2C2 MUTATED     1   1     2
  ATP2C2 WILD-TYPE   4  12   116
D168V4, multiclass
       clus
vv      ATP2C2 MUTATED ATP2C2 WILD-TYPE
  T1                 1                4
  T2                 1               12
  T3+T4              2              116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V5, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     1   3
  ATP2C2 WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    3
  ATP2C2 WILD-TYPE   31  101
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D168V6, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    1  0
  ATP2C2 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    0
  ATP2C2 WILD-TYPE   61    3
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D168V7, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    3  1
  ATP2C2 WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      3    1
  ATP2C2 WILD-TYPE   59   73
        clus
vv       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2C2 MUTATED                                     4
  ATP2C2 WILD-TYPE                                 118
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2C2 MUTATED                                       0
  ATP2C2 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2C2 MUTATED                                                  0
  ATP2C2 WILD-TYPE                                                2
D168V8, multiclass
                                                  clus
vv                                                 ATP2C2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ATP2C2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V9, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N       TCGA-HZ-A77Q 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
D168V10, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPY       TCGA-H6-8124 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATP2C2 MUTATED    4  0  0  0
  ATP2C2 WILD-TYPE 73 48  1  3
D168V11, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  R0              4               73
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2C2 MUTATED       0                         0     4
  ATP2C2 WILD-TYPE     2                         5   121
D168V13, multiclass
                           clus
vv                          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V14, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     0   4
  ATP2C2 WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      0    4
  ATP2C2 WILD-TYPE    3  100
                        clus
vv                       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(169) Variable = ANKRD30A MUTATION ANALYSIS
D169V1, survival
                    sevent
clus2                 0  1
  ANKRD30A MUTATED    4  4
  ANKRD30A WILD-TYPE 58 68
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                126 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 4                 68 
$`ANKRD30A MUTATED`
TCGA-3A-A9IC TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7M4 
       24.26         6.38        10.85        19.82         1.35        15.88 
TCGA-RB-AA9M TCGA-US-A779 
        9.40        16.80 

$`ANKRD30A WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        53.00        23.61        20.84         7.36        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK 
       14.93        17.92        21.70        16.14        10.13        21.60 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       13.68         3.12        15.32        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        27.75        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              1.35               0.13 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             24.26              75.12 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            13.365             13.745 
[1] "1.4 - 24.3 (13.4)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1"  
D169V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANKRD30A MUTATED          0        0         0         8         0        0
  ANKRD30A WILD-TYPE        4        6        20        91         4        3
D169V3, multiclass
           clus
vv          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE IA                 0                  4
  STAGE IB                 0                  6
  STAGE IIA                0                 20
  STAGE IIB                8                 91
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  ANKRD30A MUTATED     1   0     7
  ANKRD30A WILD-TYPE   4  13   111
D169V4, multiclass
       clus
vv      ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                   1                  4
  T2                   0                 13
  T3+T4                7                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V5, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    0  8
  ANKRD30A WILD-TYPE 32 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    8
  ANKRD30A WILD-TYPE   32   96
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                0                 32
  1                8                 96
[1] 2 2
[1] FALSE
D169V6, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    2  0
  ANKRD30A WILD-TYPE 60  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      2    0
  ANKRD30A WILD-TYPE   60    3
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                2                 60
  1                0                  3
[1] 2 2
[1] FALSE
D169V7, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    3  5
  ANKRD30A WILD-TYPE 59 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      3    5
  ANKRD30A WILD-TYPE   59   69
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  FEMALE                3                 59
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD30A MUTATED                                     7
  ANKRD30A WILD-TYPE                                 115
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD30A MUTATED                                       1
  ANKRD30A WILD-TYPE                                    10
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD30A MUTATED                                                  0
  ANKRD30A WILD-TYPE                                                2
D169V8, multiclass
                                                  clus
vv                                                 ANKRD30A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 ANKRD30A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V9, continuous
D169V10, continuous
                    vv
clus                 R0 R1 R2 RX
  ANKRD30A MUTATED    6  2  0  0
  ANKRD30A WILD-TYPE 71 46  1  3
D169V11, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0                6                 71
  R1                2                 46
  R2                0                  1
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD30A MUTATED       0                         0     8
  ANKRD30A WILD-TYPE     2                         5   117
D169V13, multiclass
                           clus
vv                          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    8                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V14, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    0  7
  ANKRD30A WILD-TYPE  3 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    7
  ANKRD30A WILD-TYPE    3   97
                        clus
vv                       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                7                 97
[1] 2 2
[1] FALSE

Clustering(170) Variable = MKI67 MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2              0  1
  MKI67 MUTATED    3  3
  MKI67 WILD-TYPE 59 69
  MKI67 MUTATED MKI67 WILD-TYPE 
              6             128 
  MKI67 MUTATED MKI67 WILD-TYPE 
              3              69 
$`MKI67 MUTATED`
TCGA-3A-A9I9 TCGA-FB-AAPZ TCGA-IB-7651 TCGA-IB-7888 TCGA-RB-AA9M TCGA-YY-A8LH 
       20.84        23.54        19.82        43.79         9.40        66.28 

$`MKI67 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        53.00        23.61         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       34.82        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM 
        8.78        15.45        13.68         3.12        15.32        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76         0.69 

  MKI67 MUTATED MKI67 WILD-TYPE 
           9.40            0.13 
  MKI67 MUTATED MKI67 WILD-TYPE 
          66.28           75.12 
  MKI67 MUTATED MKI67 WILD-TYPE 
         22.190          13.155 
[1] "9.4 - 66.3 (22.2)" "0.1 - 75.1 (13.2)"
[1] "hr=" "2.2"
D170V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MKI67 MUTATED          0        0         2         4         0        0
  MKI67 WILD-TYPE        4        6        18        95         4        3
D170V3, multiclass
           clus
vv          MKI67 MUTATED MKI67 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             4              95
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  MKI67 MUTATED     1   1     4
  MKI67 WILD-TYPE   4  12   114
D170V4, multiclass
       clus
vv      MKI67 MUTATED MKI67 WILD-TYPE
  T1                1               4
  T2                1              12
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V5, binary
                 cls
clus                0   1
  MKI67 MUTATED     2   4
  MKI67 WILD-TYPE  30 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      2    4
  MKI67 WILD-TYPE   30  100
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0             2              30
  1             4             100
[1] 2 2
[1] FALSE
D170V6, binary
                 cls
clus               0  1
  MKI67 MUTATED    2  0
  MKI67 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      2    0
  MKI67 WILD-TYPE   60    3
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D170V7, binary
                 cls
clus               0  1
  MKI67 MUTATED    3  3
  MKI67 WILD-TYPE 59 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      3    3
  MKI67 WILD-TYPE   59   71
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  FEMALE             3              59
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MKI67 MUTATED                                     6
  MKI67 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MKI67 MUTATED                                       0
  MKI67 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MKI67 MUTATED                                                  0
  MKI67 WILD-TYPE                                                2
D170V8, multiclass
                                                  clus
vv                                                 MKI67 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 MKI67 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V9, continuous
D170V10, continuous
[1] "Remove cluster labels:" "MKI67 MUTATED"         
clus
  MKI67 MUTATED MKI67 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-XD-AAUL 
"MKI67 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MKI67 MUTATED    6  0  0  0
  MKI67 WILD-TYPE 71 48  1  3
D170V11, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0             6              71
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MKI67 MUTATED       0                         1     5
  MKI67 WILD-TYPE     2                         4   120
D170V13, multiclass
                           clus
vv                          MKI67 MUTATED MKI67 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V14, binary
                 cls
clus               0  1
  MKI67 MUTATED    0  6
  MKI67 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      0    6
  MKI67 WILD-TYPE    3   98
                        clus
vv                       MKI67 MUTATED MKI67 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(171) Variable = FCGBP MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2              0  1
  FCGBP MUTATED    5  7
  FCGBP WILD-TYPE 57 65
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             122 
  FCGBP MUTATED FCGBP WILD-TYPE 
              7              65 
$`FCGBP MUTATED`
TCGA-2J-AAB6 TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-FB-AAQ1 TCGA-H6-8124 
        9.63         3.39         9.60        53.00         4.04        12.89 
TCGA-HZ-7922 TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUM TCGA-IB-AAUQ TCGA-XD-AAUH 
        0.13        19.82        12.00         0.26         6.02        12.99 

$`FCGBP WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9I9 
       21.44         4.70        22.49        12.95        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
        7.36        24.26        28.73        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       12.39        75.12        71.74        10.98         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM 
        3.12        17.00         5.88        11.93        24.07        14.76 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.43         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 
        5.03         1.02        13.84        19.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98         2.47        17.16        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
        0.39        13.81        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  FCGBP MUTATED FCGBP WILD-TYPE 
           0.13            0.23 
  FCGBP MUTATED FCGBP WILD-TYPE 
          53.00           75.12 
  FCGBP MUTATED FCGBP WILD-TYPE 
          9.615          14.285 
[1] "0.1 - 53.0 (9.6)"  "0.2 - 75.1 (14.3)"
[1] "hr=" "1.7"
D171V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FCGBP MUTATED          1        0         1        10         0        0
  FCGBP WILD-TYPE        3        6        19        89         4        3
D171V3, multiclass
           clus
vv          FCGBP MUTATED FCGBP WILD-TYPE
  STAGE IA              1               3
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB            10              89
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  FCGBP MUTATED     1   1    10
  FCGBP WILD-TYPE   4  12   108
D171V4, multiclass
       clus
vv      FCGBP MUTATED FCGBP WILD-TYPE
  T1                1               4
  T2                1              12
  T3+T4            10             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V5, binary
                 cls
clus               0  1
  FCGBP MUTATED    2 10
  FCGBP WILD-TYPE 30 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2   10
  FCGBP WILD-TYPE   30   94
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             2              30
  1            10              94
[1] 2 2
[1] FALSE
D171V6, binary
                 cls
clus               0  1
  FCGBP MUTATED    7  0
  FCGBP WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      7    0
  FCGBP WILD-TYPE   55    3
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             7              55
  1             0               3
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus               0  1
  FCGBP MUTATED    4  8
  FCGBP WILD-TYPE 58 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      4    8
  FCGBP WILD-TYPE   58   66
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  FEMALE             4              58
  MALE               8              66
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FCGBP MUTATED                                    12
  FCGBP WILD-TYPE                                 110
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FCGBP MUTATED                                       0
  FCGBP WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FCGBP MUTATED                                                  0
  FCGBP WILD-TYPE                                                2
D171V8, multiclass
                                                  clus
vv                                                 FCGBP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 FCGBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V9, continuous
D171V10, continuous
                 vv
clus              R0 R1 R2 RX
  FCGBP MUTATED    7  3  1  1
  FCGBP WILD-TYPE 70 45  0  2
D171V11, multiclass
    clus
vv   FCGBP MUTATED FCGBP WILD-TYPE
  R0             7              70
  R1             3              45
  R2             1               0
  RX             1               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FCGBP MUTATED       0                         0    12
  FCGBP WILD-TYPE     2                         5   113
D171V13, multiclass
                           clus
vv                          FCGBP MUTATED FCGBP WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                12             113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V14, binary
                 cls
clus               0  1
  FCGBP MUTATED    0  8
  FCGBP WILD-TYPE  3 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      0    8
  FCGBP WILD-TYPE    3   96
                        clus
vv                       FCGBP MUTATED FCGBP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8              96
[1] 2 2
[1] FALSE

Clustering(172) Variable = SRFBP1 MUTATION ANALYSIS
D172V1, survival
                  sevent
clus2               0  1
  SRFBP1 MUTATED    0  3
  SRFBP1 WILD-TYPE 62 69
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              131 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3               69 
$`SRFBP1 MUTATED`
TCGA-2L-AAQA TCGA-IB-7651 TCGA-IB-7887 
        4.70        19.82         3.62 

$`SRFBP1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
            3.62             0.13 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
           19.82            75.12 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
            4.70            13.81 
[1] "3.6 - 19.8 (4.7)"  "0.1 - 75.1 (13.8)"
[1] "hr=" "3.6"
D172V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SRFBP1 MUTATED          0        0         0         3         0        0
  SRFBP1 WILD-TYPE        4        6        20        96         4        3
D172V3, multiclass
           clus
vv          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  SRFBP1 MUTATED     0   0     3
  SRFBP1 WILD-TYPE   5  13   115
D172V4, multiclass
       clus
vv      SRFBP1 MUTATED SRFBP1 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              3              115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V5, binary
                  cls
clus                 0   1
  SRFBP1 MUTATED     0   3
  SRFBP1 WILD-TYPE  32 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      0    3
  SRFBP1 WILD-TYPE   32  101
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              0               32
  1              3              101
[1] 2 2
[1] FALSE
D172V6, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    2  0
  SRFBP1 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      2    0
  SRFBP1 WILD-TYPE   60    3
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D172V7, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    2  1
  SRFBP1 WILD-TYPE 60 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      2    1
  SRFBP1 WILD-TYPE   60   73
        clus
vv       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  FEMALE              2               60
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SRFBP1 MUTATED                                     3
  SRFBP1 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SRFBP1 MUTATED                                       0
  SRFBP1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SRFBP1 MUTATED                                                  0
  SRFBP1 WILD-TYPE                                                2
D172V8, multiclass
                                                  clus
vv                                                 SRFBP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 SRFBP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V9, continuous
D172V10, continuous
[1] "Remove cluster labels:" "SRFBP1 MUTATED"        
clus
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SRFBP1 MUTATED    1  2  0  0
  SRFBP1 WILD-TYPE 76 46  1  3
D172V11, multiclass
    clus
vv   SRFBP1 MUTATED SRFBP1 WILD-TYPE
  R0              1               76
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRFBP1 MUTATED       0                         0     3
  SRFBP1 WILD-TYPE     2                         5   122
D172V13, multiclass
                           clus
vv                          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V14, binary
                  cls
clus                 0   1
  SRFBP1 MUTATED     0   2
  SRFBP1 WILD-TYPE   3 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      0    2
  SRFBP1 WILD-TYPE    3  102
                        clus
vv                       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2              102
[1] 2 2
[1] FALSE

Clustering(173) Variable = NFKBIZ MUTATION ANALYSIS
D173V1, survival
                  sevent
clus2               0  1
  NFKBIZ MUTATED    2  2
  NFKBIZ WILD-TYPE 60 70
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               4              130 
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               2               70 
$`NFKBIZ MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-AAUO TCGA-YY-A8LH 
       10.85        19.82         7.86        66.28 

$`NFKBIZ WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38        21.60         5.26         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       49.38         4.77        21.90        15.35        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.32        11.51        12.76         0.69 

  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
            7.86             0.13 
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
           66.28            75.12 
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
          15.335           13.745 
[1] "7.9 - 66.3 (15.3)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.5"
D173V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NFKBIZ MUTATED          0        0         0         4         0        0
  NFKBIZ WILD-TYPE        4        6        20        95         4        3
D173V3, multiclass
           clus
vv          NFKBIZ MUTATED NFKBIZ WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  NFKBIZ MUTATED     0   0     4
  NFKBIZ WILD-TYPE   5  13   114
D173V4, multiclass
       clus
vv      NFKBIZ MUTATED NFKBIZ WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V5, binary
                  cls
clus                 0   1
  NFKBIZ MUTATED     0   4
  NFKBIZ WILD-TYPE  32 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIZ MUTATED      0    4
  NFKBIZ WILD-TYPE   32  100
   clus
vv  NFKBIZ MUTATED NFKBIZ WILD-TYPE
  0              0               32
  1              4              100
[1] 2 2
[1] FALSE
D173V6, binary
                  cls
clus                0  1
  NFKBIZ MUTATED    2  0
  NFKBIZ WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIZ MUTATED      2    0
  NFKBIZ WILD-TYPE   60    3
   clus
vv  NFKBIZ MUTATED NFKBIZ WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D173V7, binary
                  cls
clus                0  1
  NFKBIZ MUTATED    3  1
  NFKBIZ WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIZ MUTATED      3    1
  NFKBIZ WILD-TYPE   59   73
        clus
vv       NFKBIZ MUTATED NFKBIZ WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFKBIZ MUTATED                                     3
  NFKBIZ WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFKBIZ MUTATED                                       1
  NFKBIZ WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFKBIZ MUTATED                                                  0
  NFKBIZ WILD-TYPE                                                2
D173V8, multiclass
                                                  clus
vv                                                 NFKBIZ MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 NFKBIZ WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V9, continuous
[1] "Remove cluster labels:" "NFKBIZ MUTATED"        
clus
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
D173V10, continuous
[1] "Remove cluster labels:" "NFKBIZ MUTATED"        
clus
  NFKBIZ MUTATED NFKBIZ WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" "NFKBIZ WILD-TYPE" 
      TCGA-XD-AAUL 
"NFKBIZ WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NFKBIZ MUTATED    3  1  0  0
  NFKBIZ WILD-TYPE 74 47  1  3
D173V11, multiclass
    clus
vv   NFKBIZ MUTATED NFKBIZ WILD-TYPE
  R0              3               74
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFKBIZ MUTATED       0                         0     4
  NFKBIZ WILD-TYPE     2                         5   121
D173V13, multiclass
                           clus
vv                          NFKBIZ MUTATED NFKBIZ WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V14, binary
                  cls
clus                 0   1
  NFKBIZ MUTATED     0   4
  NFKBIZ WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIZ MUTATED      0    4
  NFKBIZ WILD-TYPE    3  100
                        clus
vv                       NFKBIZ MUTATED NFKBIZ WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(174) Variable = NBPF10 MUTATION ANALYSIS
D174V1, survival
                  sevent
clus2               0  1
  NBPF10 MUTATED    1  4
  NBPF10 WILD-TYPE 61 68
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               5              129 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4               68 
$`NBPF10 MUTATED`
TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-FB-AAQ0 TCGA-IB-7646 TCGA-IB-A5SS 
       15.06        12.39        15.55         4.77        15.12 

$`NBPF10 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       28.73        34.09        10.13        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N 
       23.54         4.04         5.03         1.02        12.89        13.84 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       19.50         0.13        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       10.85         1.08         0.23        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
        2.47        17.16        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.05        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            4.77             0.13 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           15.55            75.12 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           15.06            13.68 
[1] "4.8 - 15.6 (15.1)" "0.1 - 75.1 (13.7)"
[1] "hr=" "2.2"
D174V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NBPF10 MUTATED          0        0         1         4         0        0
  NBPF10 WILD-TYPE        4        6        19        95         4        3
D174V3, multiclass
           clus
vv          NBPF10 MUTATED NBPF10 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              4               95
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  NBPF10 MUTATED     0   0     5
  NBPF10 WILD-TYPE   5  13   113
D174V4, multiclass
       clus
vv      NBPF10 MUTATED NBPF10 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V5, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     1   4
  NBPF10 WILD-TYPE  31 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      1    4
  NBPF10 WILD-TYPE   31  100
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              1               31
  1              4              100
[1] 2 2
[1] FALSE
D174V6, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  0
  NBPF10 WILD-TYPE 60  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    0
  NBPF10 WILD-TYPE   60    3
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              2               60
  1              0                3
[1] 2 2
[1] FALSE
D174V7, binary
                  cls
clus                0  1
  NBPF10 MUTATED    1  4
  NBPF10 WILD-TYPE 61 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      1    4
  NBPF10 WILD-TYPE   61   70
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  FEMALE              1               61
  MALE                4               70
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF10 MUTATED                                     5
  NBPF10 WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF10 MUTATED                                       0
  NBPF10 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF10 MUTATED                                                  0
  NBPF10 WILD-TYPE                                                2
D174V8, multiclass
                                                  clus
vv                                                 NBPF10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 NBPF10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V9, continuous
[1] "Remove cluster labels:" "NBPF10 MUTATED"        
clus
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
D174V10, continuous
[1] "Remove cluster labels:" "NBPF10 MUTATED"        
clus
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-7886       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NBPF10 MUTATED    4  1  0  0
  NBPF10 WILD-TYPE 73 47  1  3
D174V11, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  R0              4               73
  R1              1               47
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED       0                         0     5
  NBPF10 WILD-TYPE     2                         5   120
D174V13, multiclass
                           clus
vv                          NBPF10 MUTATED NBPF10 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V14, binary
                  cls
clus                0  1
  NBPF10 MUTATED    0  5
  NBPF10 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      0    5
  NBPF10 WILD-TYPE    3   99
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(175) Variable = ZNF358 MUTATION ANALYSIS
D175V1, survival
                  sevent
clus2               0  1
  ZNF358 MUTATED    1  3
  ZNF358 WILD-TYPE 61 69
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              130 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               3               69 
$`ZNF358 MUTATED`
TCGA-2L-AAQJ TCGA-HZ-7926 TCGA-HZ-A77Q TCGA-IB-7651 
       12.95        17.03         1.08        19.82 

$`ZNF358 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       12.89        13.84        19.50         0.13        20.19        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  ZNF358 MUTATED ZNF358 WILD-TYPE 
            1.08             0.13 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
           19.82            75.12 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
          14.990           13.745 
[1] "1.1 - 19.8 (15.0)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.7"
D175V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF358 MUTATED          0        0         0         3         1        0
  ZNF358 WILD-TYPE        4        6        20        96         3        3
D175V3, multiclass
           clus
vv          ZNF358 MUTATED ZNF358 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              3               96
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF358 MUTATED     0   0     4
  ZNF358 WILD-TYPE   5  13   114
D175V4, multiclass
       clus
vv      ZNF358 MUTATED ZNF358 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V5, binary
                  cls
clus                 0   1
  ZNF358 MUTATED     1   3
  ZNF358 WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      1    3
  ZNF358 WILD-TYPE   31  101
   clus
vv  ZNF358 MUTATED ZNF358 WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D175V6, binary
                  cls
clus                0  1
  ZNF358 MUTATED    1  0
  ZNF358 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      1    0
  ZNF358 WILD-TYPE   61    3
   clus
vv  ZNF358 MUTATED ZNF358 WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D175V7, binary
                  cls
clus                0  1
  ZNF358 MUTATED    3  1
  ZNF358 WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      3    1
  ZNF358 WILD-TYPE   59   73
        clus
vv       ZNF358 MUTATED ZNF358 WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF358 MUTATED                                     3
  ZNF358 WILD-TYPE                                 119
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF358 MUTATED                                       1
  ZNF358 WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF358 MUTATED                                                  0
  ZNF358 WILD-TYPE                                                2
D175V8, multiclass
                                                  clus
vv                                                 ZNF358 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF358 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V9, continuous
[1] "Remove cluster labels:" "ZNF358 MUTATED"        
clus
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               2               46 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887       TCGA-IB-7891 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP       TCGA-US-A774 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
D175V10, continuous
[1] "Remove cluster labels:" "ZNF358 MUTATED"        
clus
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               2               37 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7891 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UF 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI       TCGA-XD-AAUL 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-YY-A8LH 
"ZNF358 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF358 MUTATED    2  1  0  1
  ZNF358 WILD-TYPE 75 47  1  2
D175V11, multiclass
    clus
vv   ZNF358 MUTATED ZNF358 WILD-TYPE
  R0              2               75
  R1              1               47
  R2              0                1
  RX              1                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF358 MUTATED       0                         1     3
  ZNF358 WILD-TYPE     2                         4   122
D175V13, multiclass
                           clus
vv                          ZNF358 MUTATED ZNF358 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V14, binary
                  cls
clus                 0   1
  ZNF358 MUTATED     0   3
  ZNF358 WILD-TYPE   3 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      0    3
  ZNF358 WILD-TYPE    3  101
                        clus
vv                       ZNF358 MUTATED ZNF358 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              101
[1] 2 2
[1] FALSE

Clustering(176) Variable = HIST1H2BK MUTATION ANALYSIS
D176V1, survival
                     sevent
clus2                  0  1
  HIST1H2BK MUTATED    1  1
  HIST1H2BK WILD-TYPE 61 71
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  2                 132 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  1                  71 
$`HIST1H2BK MUTATED`
TCGA-S4-A8RO TCGA-US-A77G 
       17.26         0.39 

$`HIST1H2BK WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RP 
       13.68         3.12        15.32         9.40        21.24        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        27.75        16.80        14.14        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
               0.39                0.13 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
              17.26               75.12 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
              8.825              13.745 
[1] "0.4 - 17.3 (8.8)"  "0.1 - 75.1 (13.7)"
[1] "Remove cluster labels:" "HIST1H2BK MUTATED"     
D176V2, continuous
                     vv
clus                  STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HIST1H2BK MUTATED          0        0         0         3         0        0
  HIST1H2BK WILD-TYPE        4        6        20        96         4        3
D176V3, multiclass
           clus
vv          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  STAGE IA                  0                   4
  STAGE IB                  0                   6
  STAGE IIA                 0                  20
  STAGE IIB                 3                  96
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2 T3+T4
  HIST1H2BK MUTATED     0   0     3
  HIST1H2BK WILD-TYPE   5  13   115
D176V4, multiclass
       clus
vv      HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  T1                    0                   5
  T2                    0                  13
  T3+T4                 3                 115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V5, binary
                     cls
clus                    0   1
  HIST1H2BK MUTATED     0   3
  HIST1H2BK WILD-TYPE  32 101
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      0    3
  HIST1H2BK WILD-TYPE   32  101
   clus
vv  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  0                 0                  32
  1                 3                 101
[1] 2 2
[1] FALSE
D176V6, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    0  0
  HIST1H2BK WILD-TYPE 62  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      0    0
  HIST1H2BK WILD-TYPE   62    3
D176V7, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    2  1
  HIST1H2BK WILD-TYPE 60 73
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      2    1
  HIST1H2BK WILD-TYPE   60   73
        clus
vv       HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  FEMALE                 2                  60
  MALE                   1                  73
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H2BK MUTATED                                     3
  HIST1H2BK WILD-TYPE                                 119
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H2BK MUTATED                                       0
  HIST1H2BK WILD-TYPE                                    11
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H2BK MUTATED                                                  0
  HIST1H2BK WILD-TYPE                                                2
D176V8, multiclass
                                                  clus
vv                                                 HIST1H2BK MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
                                                  clus
vv                                                 HIST1H2BK WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V9, continuous
D176V10, continuous
                     vv
clus                  R0 R1 R2 RX
  HIST1H2BK MUTATED    2  1  0  0
  HIST1H2BK WILD-TYPE 75 47  1  3
D176V11, multiclass
    clus
vv   HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  R0                 2                  75
  R1                 1                  47
  R2                 0                   1
  RX                 0                   3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V12, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BK MUTATED       0                         0     3
  HIST1H2BK WILD-TYPE     2                         5   122
D176V13, multiclass
                           clus
vv                          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  ASIAN                                     0                   2
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     3                 122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V14, binary
                     cls
clus                    0   1
  HIST1H2BK MUTATED     1   2
  HIST1H2BK WILD-TYPE   2 102
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      1    2
  HIST1H2BK WILD-TYPE    2  102
                        clus
vv                       HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  HISPANIC OR LATINO                     1                   2
  NOT HISPANIC OR LATINO                 2                 102
[1] 2 2
[1] FALSE

Clustering(177) Variable = DDB1 MUTATION ANALYSIS
D177V1, survival
                sevent
clus2             0  1
  DDB1 MUTATED    3  2
  DDB1 WILD-TYPE 59 70
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            129 
  DDB1 MUTATED DDB1 WILD-TYPE 
             2             70 
$`DDB1 MUTATED`
TCGA-HZ-A77Q TCGA-IB-7645 TCGA-IB-7651 TCGA-Q3-A5QY TCGA-YY-A8LH 
        1.08        49.38        19.82        13.68        66.28 

$`DDB1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38        21.60         5.26        10.85         0.23        12.95 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76         0.69 

  DDB1 MUTATED DDB1 WILD-TYPE 
          1.08           0.13 
  DDB1 MUTATED DDB1 WILD-TYPE 
         66.28          75.12 
  DDB1 MUTATED DDB1 WILD-TYPE 
         19.82          13.32 
[1] "1.1 - 66.3 (19.8)" "0.1 - 75.1 (13.3)"
[1] "hr=" "2.5"
D177V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DDB1 MUTATED          0        0         0         5         0        0
  DDB1 WILD-TYPE        4        6        20        94         4        3
D177V3, multiclass
           clus
vv          DDB1 MUTATED DDB1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            5             94
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  DDB1 MUTATED     0   0     5
  DDB1 WILD-TYPE   5  13   113
D177V4, multiclass
       clus
vv      DDB1 MUTATED DDB1 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            5            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V5, binary
                cls
clus              0  1
  DDB1 MUTATED    0  5
  DDB1 WILD-TYPE 32 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      0    5
  DDB1 WILD-TYPE   32   99
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            0             32
  1            5             99
[1] 2 2
[1] FALSE
D177V6, binary
                cls
clus              0  1
  DDB1 MUTATED    2  0
  DDB1 WILD-TYPE 60  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      2    0
  DDB1 WILD-TYPE   60    3
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            2             60
  1            0              3
[1] 2 2
[1] FALSE
D177V7, binary
                cls
clus              0  1
  DDB1 MUTATED    4  1
  DDB1 WILD-TYPE 58 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      4    1
  DDB1 WILD-TYPE   58   73
        clus
vv       DDB1 MUTATED DDB1 WILD-TYPE
  FEMALE            4             58
  MALE              1             73
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DDB1 MUTATED                                     4
  DDB1 WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DDB1 MUTATED                                       1
  DDB1 WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DDB1 MUTATED                                                  0
  DDB1 WILD-TYPE                                                2
D177V8, multiclass
                                                  clus
vv                                                 DDB1 MUTATED DDB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V9, continuous
D177V10, continuous
                vv
clus             R0 R1 R2 RX
  DDB1 MUTATED    5  0  0  0
  DDB1 WILD-TYPE 72 48  1  3
D177V11, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  R0            5             72
  R1            0             48
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDB1 MUTATED       0                         0     4
  DDB1 WILD-TYPE     2                         5   121
D177V13, multiclass
                           clus
vv                          DDB1 MUTATED DDB1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V14, binary
                cls
clus               0   1
  DDB1 MUTATED     0   4
  DDB1 WILD-TYPE   3 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      0    4
  DDB1 WILD-TYPE    3  100
                        clus
vv                       DDB1 MUTATED DDB1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            100
[1] 2 2
[1] FALSE

Clustering(178) Variable = BVES MUTATION ANALYSIS
D178V1, survival
                sevent
clus2             0  1
  BVES MUTATED    2  2
  BVES WILD-TYPE 60 70
  BVES MUTATED BVES WILD-TYPE 
             4            130 
  BVES MUTATED BVES WILD-TYPE 
             2             70 
$`BVES MUTATED`
TCGA-2J-AABR TCGA-IB-7646 TCGA-IB-7651 TCGA-XD-AAUL 
       14.40         4.77        19.82        13.32 

$`BVES WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        22.26        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       49.38        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  BVES MUTATED BVES WILD-TYPE 
          4.77           0.13 
  BVES MUTATED BVES WILD-TYPE 
         19.82          75.12 
  BVES MUTATED BVES WILD-TYPE 
        13.860         13.745 
[1] "4.8 - 19.8 (13.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D178V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BVES MUTATED          0        0         2         2         0        0
  BVES WILD-TYPE        4        6        18        97         4        3
D178V3, multiclass
           clus
vv          BVES MUTATED BVES WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            2             18
  STAGE IIB            2             97
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  BVES MUTATED     0   0     4
  BVES WILD-TYPE   5  13   114
D178V4, multiclass
       clus
vv      BVES MUTATED BVES WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            4            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V5, binary
                cls
clus               0   1
  BVES MUTATED     2   2
  BVES WILD-TYPE  30 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      2    2
  BVES WILD-TYPE   30  102
   clus
vv  BVES MUTATED BVES WILD-TYPE
  0            2             30
  1            2            102
[1] 2 2
[1] FALSE
D178V6, binary
                cls
clus              0  1
  BVES MUTATED    3  0
  BVES WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      3    0
  BVES WILD-TYPE   59    3
   clus
vv  BVES MUTATED BVES WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D178V7, binary
                cls
clus              0  1
  BVES MUTATED    2  2
  BVES WILD-TYPE 60 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      2    2
  BVES WILD-TYPE   60   72
        clus
vv       BVES MUTATED BVES WILD-TYPE
  FEMALE            2             60
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BVES MUTATED                                     4
  BVES WILD-TYPE                                 118
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BVES MUTATED                                       0
  BVES WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BVES MUTATED                                                  0
  BVES WILD-TYPE                                                2
D178V8, multiclass
                                                  clus
vv                                                 BVES MUTATED BVES WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V9, continuous
[1] "Remove cluster labels:" "BVES MUTATED"          
clus
  BVES MUTATED BVES WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-US-A774     TCGA-YY-A8LH 
"BVES WILD-TYPE" "BVES WILD-TYPE" 
D178V10, continuous
[1] "Remove cluster labels:" "BVES MUTATED"          
clus
  BVES MUTATED BVES WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-YY-A8LH 
"BVES WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BVES MUTATED    3  1  0  0
  BVES WILD-TYPE 74 47  1  3
D178V11, multiclass
    clus
vv   BVES MUTATED BVES WILD-TYPE
  R0            3             74
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BVES MUTATED       0                         0     4
  BVES WILD-TYPE     2                         5   121
D178V13, multiclass
                           clus
vv                          BVES MUTATED BVES WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V14, binary
                cls
clus               0   1
  BVES MUTATED     0   3
  BVES WILD-TYPE   3 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      0    3
  BVES WILD-TYPE    3  101
                        clus
vv                       BVES MUTATED BVES WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            101
[1] 2 2
[1] FALSE

Clustering(179) Variable = SLC26A3 MUTATION ANALYSIS
D179V1, survival
                   sevent
clus2                0  1
  SLC26A3 MUTATED    0  3
  SLC26A3 WILD-TYPE 62 69
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                3               131 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                3                69 
$`SLC26A3 MUTATED`
TCGA-3A-A9IZ TCGA-IB-7649 TCGA-IB-7651 
       10.13        15.35        19.82 

$`SLC26A3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       28.73        15.06        34.09        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
       49.38         4.77        21.90        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
            10.13              0.13 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
            19.82             75.12 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
            15.35             13.68 
[1] "10.1 - 19.8 (15.3)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "2.1"
D179V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SLC26A3 MUTATED          0        0         0         3         0        0
  SLC26A3 WILD-TYPE        4        6        20        96         4        3
D179V3, multiclass
           clus
vv          SLC26A3 MUTATED SLC26A3 WILD-TYPE
  STAGE IA                0                 4
  STAGE IB                0                 6
  STAGE IIA               0                20
  STAGE IIB               3                96
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SLC26A3 MUTATED     0   0     3
  SLC26A3 WILD-TYPE   5  13   115
D179V4, multiclass
       clus
vv      SLC26A3 MUTATED SLC26A3 WILD-TYPE
  T1                  0                 5
  T2                  0                13
  T3+T4               3               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V5, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     0   3
  SLC26A3 WILD-TYPE  32 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      0    3
  SLC26A3 WILD-TYPE   32  101
   clus
vv  SLC26A3 MUTATED SLC26A3 WILD-TYPE
  0               0                32
  1               3               101
[1] 2 2
[1] FALSE
D179V6, binary
                   cls
clus                 0  1
  SLC26A3 MUTATED    2  0
  SLC26A3 WILD-TYPE 60  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      2    0
  SLC26A3 WILD-TYPE   60    3
   clus
vv  SLC26A3 MUTATED SLC26A3 WILD-TYPE
  0               2                60
  1               0                 3
[1] 2 2
[1] FALSE
D179V7, binary
                   cls
clus                 0  1
  SLC26A3 MUTATED    2  1
  SLC26A3 WILD-TYPE 60 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      2    1
  SLC26A3 WILD-TYPE   60   73
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  FEMALE               2                60
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC26A3 MUTATED                                     3
  SLC26A3 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC26A3 MUTATED                                       0
  SLC26A3 WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC26A3 MUTATED                                                  0
  SLC26A3 WILD-TYPE                                                2
D179V8, multiclass
                                                  clus
vv                                                 SLC26A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SLC26A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V9, continuous
[1] "Remove cluster labels:" "SLC26A3 MUTATED"       
clus
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                2                46 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-YY-A8LH 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
D179V10, continuous
[1] "Remove cluster labels:" "SLC26A3 MUTATED"       
clus
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                2                37 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A4P6 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS        TCGA-FB-AAPY 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-H6-8124        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7891 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC26A3 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC26A3 MUTATED    1  2  0  0
  SLC26A3 WILD-TYPE 76 46  1  3
D179V11, multiclass
    clus
vv   SLC26A3 MUTATED SLC26A3 WILD-TYPE
  R0               1                76
  R1               2                46
  R2               0                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC26A3 MUTATED       0                         0     2
  SLC26A3 WILD-TYPE     2                         5   123
D179V13, multiclass
[1] "Remove cluster labels:" "SLC26A3 MUTATED"       
clus
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                2               130 
       TCGA-2J-AAB1        TCGA-2J-AAB4        TCGA-2J-AAB6        TCGA-2J-AAB8 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-2J-AAB9        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-2J-AABH        TCGA-2J-AABK        TCGA-2J-AABO        TCGA-2J-AABR 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-2J-AABU        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-2L-AAQI        TCGA-2L-AAQJ        TCGA-2L-AAQL        TCGA-3A-A9I5 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-3A-A9I7        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IC 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-3A-A9IH        TCGA-3A-A9IU        TCGA-3A-A9IX        TCGA-3A-A9J0 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-3E-AAAY        TCGA-3E-AAAZ        TCGA-F2-6879        TCGA-F2-A44G 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-F2-A44H        TCGA-F2-A7TX        TCGA-F2-A8YN        TCGA-FB-A4P5 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-A4P6        TCGA-FB-A545        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPU        TCGA-FB-AAPY        TCGA-FB-AAPZ 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-FB-AAQ0        TCGA-FB-AAQ1        TCGA-FB-AAQ2        TCGA-FB-AAQ3 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-H6-8124        TCGA-H6-A45N        TCGA-HZ-7919        TCGA-HZ-7922 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-7925        TCGA-HZ-7926        TCGA-HZ-8001        TCGA-HZ-8002 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-8003        TCGA-HZ-8005        TCGA-HZ-8315        TCGA-HZ-8317 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-8519        TCGA-HZ-8636        TCGA-HZ-8637        TCGA-HZ-A49G 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-A49H        TCGA-HZ-A49I        TCGA-HZ-A4BH        TCGA-HZ-A4BK 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-A77O        TCGA-HZ-A77P        TCGA-HZ-A77Q        TCGA-HZ-A8P0 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7644        TCGA-IB-7646        TCGA-IB-7647 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-7652        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-7888        TCGA-IB-7889        TCGA-IB-7891        TCGA-IB-7893 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-7897        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SO 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-A5SP        TCGA-IB-A5SQ        TCGA-IB-A5SS        TCGA-IB-A5ST 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7LX        TCGA-IB-A7M4 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-AAUM        TCGA-IB-AAUN        TCGA-IB-AAUO        TCGA-IB-AAUP 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUR        TCGA-IB-AAUS        TCGA-IB-AAUT 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-LB-A7SX        TCGA-LB-A8F3        TCGA-LB-A9Q5 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-PZ-A5RE        TCGA-Q3-A5QY        TCGA-Q3-AA2A 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-RB-A7B8        TCGA-RB-AA9M        TCGA-S4-A8RM        TCGA-S4-A8RO 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-US-A776        TCGA-US-A779 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-US-A77E        TCGA-US-A77G        TCGA-XD-AAUG        TCGA-XD-AAUH 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YB-A89D        TCGA-YH-A8SY 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-YY-A8LH        TCGA-Z5-AAPL 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
D179V14, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     1   1
  SLC26A3 WILD-TYPE   2 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      1    1
  SLC26A3 WILD-TYPE    2  103
                        clus
vv                       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               1               103
[1] 2 2
[1] FALSE

Clustering(180) Variable = CMYA5 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2              0  1
  CMYA5 MUTATED    1  6
  CMYA5 WILD-TYPE 61 66
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              7             127 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              6              66 
$`CMYA5 MUTATED`
TCGA-2J-AABA TCGA-2J-AABH TCGA-HZ-8002 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-AAUQ 
       19.96        22.26        12.03        15.35        19.82         6.02 
TCGA-US-A779 
       16.80 

$`CMYA5 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.72        15.91        14.47        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       21.90        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
        7.86        14.17        11.11         7.40         9.44         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       23.08        22.85        27.75        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  CMYA5 MUTATED CMYA5 WILD-TYPE 
           6.02            0.13 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
          22.26           75.12 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
          16.80           13.32 
[1] "6.0 - 22.3 (16.8)" "0.1 - 75.1 (13.3)"
[1] "hr=" "1.6"
D180V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CMYA5 MUTATED          0        0         1         6         0        0
  CMYA5 WILD-TYPE        4        6        19        93         4        3
D180V3, multiclass
           clus
vv          CMYA5 MUTATED CMYA5 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             6              93
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CMYA5 MUTATED     0   0     7
  CMYA5 WILD-TYPE   5  13   111
D180V4, multiclass
       clus
vv      CMYA5 MUTATED CMYA5 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             7             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V5, binary
                 cls
clus               0  1
  CMYA5 MUTATED    1  6
  CMYA5 WILD-TYPE 31 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      1    6
  CMYA5 WILD-TYPE   31   98
   clus
vv  CMYA5 MUTATED CMYA5 WILD-TYPE
  0             1              31
  1             6              98
[1] 2 2
[1] FALSE
D180V6, binary
                 cls
clus               0  1
  CMYA5 MUTATED    5  0
  CMYA5 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      5    0
  CMYA5 WILD-TYPE   57    3
   clus
vv  CMYA5 MUTATED CMYA5 WILD-TYPE
  0             5              57
  1             0               3
[1] 2 2
[1] FALSE
D180V7, binary
                 cls
clus               0  1
  CMYA5 MUTATED    3  4
  CMYA5 WILD-TYPE 59 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      3    4
  CMYA5 WILD-TYPE   59   70
        clus
vv       CMYA5 MUTATED CMYA5 WILD-TYPE
  FEMALE             3              59
  MALE               4              70
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CMYA5 MUTATED                                     6
  CMYA5 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CMYA5 MUTATED                                       1
  CMYA5 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CMYA5 MUTATED                                                  0
  CMYA5 WILD-TYPE                                                2
D180V8, multiclass
                                                  clus
vv                                                 CMYA5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CMYA5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V9, continuous
D180V10, continuous
                 vv
clus              R0 R1 R2 RX
  CMYA5 MUTATED    4  3  0  0
  CMYA5 WILD-TYPE 73 45  1  3
D180V11, multiclass
    clus
vv   CMYA5 MUTATED CMYA5 WILD-TYPE
  R0             4              73
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CMYA5 MUTATED       0                         0     6
  CMYA5 WILD-TYPE     2                         5   119
D180V13, multiclass
                           clus
vv                          CMYA5 MUTATED CMYA5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V14, binary
                 cls
clus                0   1
  CMYA5 MUTATED     0   4
  CMYA5 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      0    4
  CMYA5 WILD-TYPE    3  100
                        clus
vv                       CMYA5 MUTATED CMYA5 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(181) Variable = CHSY3 MUTATION ANALYSIS
D181V1, survival
                 sevent
clus2              0  1
  CHSY3 MUTATED    2  3
  CHSY3 WILD-TYPE 60 69
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              5             129 
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              3              69 
$`CHSY3 MUTATED`
TCGA-2J-AABR TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-7888 TCGA-US-A77G 
       14.40         7.50        19.82        43.79         0.39 

$`CHSY3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        22.26        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76        12.43        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44         8.05        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       14.14        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  CHSY3 MUTATED CHSY3 WILD-TYPE 
           0.39            0.13 
  CHSY3 MUTATED CHSY3 WILD-TYPE 
          43.79           75.12 
  CHSY3 MUTATED CHSY3 WILD-TYPE 
          14.40           13.68 
[1] "0.4 - 43.8 (14.4)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1"  
D181V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CHSY3 MUTATED          0        0         2         3         0        0
  CHSY3 WILD-TYPE        4        6        18        96         4        3
D181V3, multiclass
           clus
vv          CHSY3 MUTATED CHSY3 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             2              18
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CHSY3 MUTATED     0   1     4
  CHSY3 WILD-TYPE   5  12   114
D181V4, multiclass
       clus
vv      CHSY3 MUTATED CHSY3 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             4             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V5, binary
                 cls
clus                0   1
  CHSY3 MUTATED     2   3
  CHSY3 WILD-TYPE  30 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHSY3 MUTATED      2    3
  CHSY3 WILD-TYPE   30  101
   clus
vv  CHSY3 MUTATED CHSY3 WILD-TYPE
  0             2              30
  1             3             101
[1] 2 2
[1] FALSE
D181V6, binary
                 cls
clus               0  1
  CHSY3 MUTATED    3  0
  CHSY3 WILD-TYPE 59  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHSY3 MUTATED      3    0
  CHSY3 WILD-TYPE   59    3
   clus
vv  CHSY3 MUTATED CHSY3 WILD-TYPE
  0             3              59
  1             0               3
[1] 2 2
[1] FALSE
D181V7, binary
                 cls
clus               0  1
  CHSY3 MUTATED    4  1
  CHSY3 WILD-TYPE 58 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHSY3 MUTATED      4    1
  CHSY3 WILD-TYPE   58   73
        clus
vv       CHSY3 MUTATED CHSY3 WILD-TYPE
  FEMALE             4              58
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHSY3 MUTATED                                     5
  CHSY3 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHSY3 MUTATED                                       0
  CHSY3 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHSY3 MUTATED                                                  0
  CHSY3 WILD-TYPE                                                2
D181V8, multiclass
                                                  clus
vv                                                 CHSY3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CHSY3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V9, continuous
[1] "Remove cluster labels:" "CHSY3 MUTATED"         
clus
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              2              46 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
D181V10, continuous
[1] "Remove cluster labels:" "CHSY3 MUTATED"         
clus
  CHSY3 MUTATED CHSY3 WILD-TYPE 
              2              37 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPY      TCGA-H6-8124 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" "CHSY3 WILD-TYPE" 
     TCGA-YY-A8LH 
"CHSY3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CHSY3 MUTATED    5  0  0  0
  CHSY3 WILD-TYPE 72 48  1  3
D181V11, multiclass
    clus
vv   CHSY3 MUTATED CHSY3 WILD-TYPE
  R0             5              72
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHSY3 MUTATED       0                         1     4
  CHSY3 WILD-TYPE     2                         4   121
D181V13, multiclass
                           clus
vv                          CHSY3 MUTATED CHSY3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V14, binary
                 cls
clus                0   1
  CHSY3 MUTATED     0   4
  CHSY3 WILD-TYPE   3 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHSY3 MUTATED      0    4
  CHSY3 WILD-TYPE    3  100
                        clus
vv                       CHSY3 MUTATED CHSY3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             100
[1] 2 2
[1] FALSE

Clustering(182) Variable = AGAP6 MUTATION ANALYSIS
D182V1, survival
                 sevent
clus2              0  1
  AGAP6 MUTATED    4  3
  AGAP6 WILD-TYPE 58 69
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             127 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              3              69 
$`AGAP6 MUTATED`
TCGA-2J-AABR TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-8127 TCGA-IB-A5SS 
       14.40        21.60         5.26        19.82        17.16        15.12 
TCGA-IB-A6UF 
       21.90 

$`AGAP6 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        22.26        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU 
       11.93        24.07        14.76        12.43         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       12.89        13.84        19.50         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG 
        2.47        12.00        15.85         7.20        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
           5.26            0.13 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          21.90           75.12 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          17.16           12.99 
[1] "5.3 - 21.9 (17.2)" "0.1 - 75.1 (13.0)"
[1] "hr=" "1.4"
D182V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AGAP6 MUTATED          0        0         1         6         0        0
  AGAP6 WILD-TYPE        4        6        19        93         4        3
D182V3, multiclass
           clus
vv          AGAP6 MUTATED AGAP6 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             1              19
  STAGE IIB             6              93
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  AGAP6 MUTATED     0   1     6
  AGAP6 WILD-TYPE   5  12   112
D182V4, multiclass
       clus
vv      AGAP6 MUTATED AGAP6 WILD-TYPE
  T1                0               5
  T2                1              12
  T3+T4             6             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V5, binary
                 cls
clus               0  1
  AGAP6 MUTATED    1  6
  AGAP6 WILD-TYPE 31 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      1    6
  AGAP6 WILD-TYPE   31   98
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             1              31
  1             6              98
[1] 2 2
[1] FALSE
D182V6, binary
                 cls
clus               0  1
  AGAP6 MUTATED    5  0
  AGAP6 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      5    0
  AGAP6 WILD-TYPE   57    3
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             5              57
  1             0               3
[1] 2 2
[1] FALSE
D182V7, binary
                 cls
clus               0  1
  AGAP6 MUTATED    4  3
  AGAP6 WILD-TYPE 58 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    3
  AGAP6 WILD-TYPE   58   71
        clus
vv       AGAP6 MUTATED AGAP6 WILD-TYPE
  FEMALE             4              58
  MALE               3              71
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AGAP6 MUTATED                                     6
  AGAP6 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AGAP6 MUTATED                                       1
  AGAP6 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AGAP6 MUTATED                                                  0
  AGAP6 WILD-TYPE                                                2
D182V8, multiclass
                                                  clus
vv                                                 AGAP6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 AGAP6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V9, continuous
D182V10, continuous
                 vv
clus              R0 R1 R2 RX
  AGAP6 MUTATED    4  3  0  0
  AGAP6 WILD-TYPE 73 45  1  3
D182V11, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  R0             4              73
  R1             3              45
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AGAP6 MUTATED       0                         0     7
  AGAP6 WILD-TYPE     2                         5   118
D182V13, multiclass
                           clus
vv                          AGAP6 MUTATED AGAP6 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V14, binary
                 cls
clus               0  1
  AGAP6 MUTATED    0  6
  AGAP6 WILD-TYPE  3 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      0    6
  AGAP6 WILD-TYPE    3   98
                        clus
vv                       AGAP6 MUTATED AGAP6 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              98
[1] 2 2
[1] FALSE

Clustering(183) Variable = NGF MUTATION ANALYSIS
D183V1, survival
               sevent
clus2            0  1
  NGF MUTATED    3  1
  NGF WILD-TYPE 59 71
  NGF MUTATED NGF WILD-TYPE 
            4           130 
  NGF MUTATED NGF WILD-TYPE 
            1            71 
$`NGF MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-YB-A89D TCGA-YH-A8SY 
       19.82        41.33        11.51        12.76 

$`NGF WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        66.28         0.69 

  NGF MUTATED NGF WILD-TYPE 
        11.51          0.13 
  NGF MUTATED NGF WILD-TYPE 
        41.33         75.12 
  NGF MUTATED NGF WILD-TYPE 
       16.290        13.745 
[1] "11.5 - 41.3 (16.3)" "0.1 - 75.1 (13.7)" 
[1] "hr=" "2.9"
D183V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NGF MUTATED          0        0         0         3         1        0
  NGF WILD-TYPE        4        6        20        96         3        3
D183V3, multiclass
           clus
vv          NGF MUTATED NGF WILD-TYPE
  STAGE IA            0             4
  STAGE IB            0             6
  STAGE IIA           0            20
  STAGE IIB           3            96
  STAGE III           1             3
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  NGF MUTATED     0   0     4
  NGF WILD-TYPE   5  13   114
D183V4, multiclass
       clus
vv      NGF MUTATED NGF WILD-TYPE
  T1              0             5
  T2              0            13
  T3+T4           4           114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V5, binary
               cls
clus              0   1
  NGF MUTATED     0   4
  NGF WILD-TYPE  32 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      0    4
  NGF WILD-TYPE   32  100
   clus
vv  NGF MUTATED NGF WILD-TYPE
  0           0            32
  1           4           100
[1] 2 2
[1] FALSE
D183V6, binary
               cls
clus             0  1
  NGF MUTATED    2  0
  NGF WILD-TYPE 60  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    0
  NGF WILD-TYPE   60    3
   clus
vv  NGF MUTATED NGF WILD-TYPE
  0           2            60
  1           0             3
[1] 2 2
[1] FALSE
D183V7, binary
               cls
clus             0  1
  NGF MUTATED    3  1
  NGF WILD-TYPE 59 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    1
  NGF WILD-TYPE   59   73
        clus
vv       NGF MUTATED NGF WILD-TYPE
  FEMALE           3            59
  MALE             1            73
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NGF MUTATED                                     3
  NGF WILD-TYPE                                 119
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NGF MUTATED                                       0
  NGF WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NGF MUTATED                                                  0
  NGF WILD-TYPE                                                2
D183V8, multiclass
                                                  clus
vv                                                 NGF MUTATED NGF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        3           119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V9, continuous
[1] "Remove cluster labels:" "NGF MUTATED"           
clus
  NGF MUTATED NGF WILD-TYPE 
            2            46 
   TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-FB-A78T    TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-H6-A45N 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891    TCGA-IB-8126    TCGA-IB-8127 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU    TCGA-LB-A7SX    TCGA-LB-A9Q5 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP    TCGA-US-A774    TCGA-XD-AAUL 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-YY-A8LH 
"NGF WILD-TYPE" 
D183V10, continuous
[1] "Remove cluster labels:" "NGF MUTATED"           
clus
  NGF MUTATED NGF WILD-TYPE 
            2            37 
   TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO    TCGA-3A-A9IB 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM    TCGA-FB-A78T 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-HZ-A77Q    TCGA-HZ-A8P0 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649    TCGA-IB-7886    TCGA-IB-7891 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-LB-A7SX 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-US-A774    TCGA-XD-AAUI 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-YY-A8LH 
"NGF WILD-TYPE" "NGF WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  NGF MUTATED    3  0  0  0
  NGF WILD-TYPE 74 48  1  3
D183V11, multiclass
    clus
vv   NGF MUTATED NGF WILD-TYPE
  R0           3            74
  R1           0            48
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NGF MUTATED       0                         0     4
  NGF WILD-TYPE     2                         5   121
D183V13, multiclass
                           clus
vv                          NGF MUTATED NGF WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V14, binary
               cls
clus              0   1
  NGF MUTATED     0   4
  NGF WILD-TYPE   3 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      0    4
  NGF WILD-TYPE    3  100
                        clus
vv                       NGF MUTATED NGF WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4           100
[1] 2 2
[1] FALSE

Clustering(184) Variable = SARS2 MUTATION ANALYSIS
D184V1, survival
                 sevent
clus2              0  1
  SARS2 MUTATED    1  2
  SARS2 WILD-TYPE 61 70
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             131 
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              70 
$`SARS2 MUTATED`
TCGA-2J-AAB1 TCGA-FB-A78T TCGA-RB-A7B8 
        2.17        12.43        15.32 

$`SARS2 WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        22.26        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       53.00        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
       10.98         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.93        24.07        14.76         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       11.11         7.40         9.44         8.05        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  SARS2 MUTATED SARS2 WILD-TYPE 
           2.17            0.13 
  SARS2 MUTATED SARS2 WILD-TYPE 
          15.32           75.12 
  SARS2 MUTATED SARS2 WILD-TYPE 
          12.43           13.81 
[1] "2.2 - 15.3 (12.4)" "0.1 - 75.1 (13.8)"
[1] "hr=" "2.4"
D184V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SARS2 MUTATED          0        0         0         3         0        0
  SARS2 WILD-TYPE        4        6        20        96         4        3
D184V3, multiclass
           clus
vv          SARS2 MUTATED SARS2 WILD-TYPE
  STAGE IA              0               4
  STAGE IB              0               6
  STAGE IIA             0              20
  STAGE IIB             3              96
  STAGE III             0               4
  STAGE IV              0               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SARS2 MUTATED     0   0     3
  SARS2 WILD-TYPE   5  13   115
D184V4, multiclass
       clus
vv      SARS2 MUTATED SARS2 WILD-TYPE
  T1                0               5
  T2                0              13
  T3+T4             3             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V5, binary
                 cls
clus                0   1
  SARS2 MUTATED     0   3
  SARS2 WILD-TYPE  32 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    3
  SARS2 WILD-TYPE   32  101
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             0              32
  1             3             101
[1] 2 2
[1] FALSE
D184V6, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  0
  SARS2 WILD-TYPE 60  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    0
  SARS2 WILD-TYPE   60    3
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             2              60
  1             0               3
[1] 2 2
[1] FALSE
D184V7, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  1
  SARS2 WILD-TYPE 60 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    1
  SARS2 WILD-TYPE   60   73
        clus
vv       SARS2 MUTATED SARS2 WILD-TYPE
  FEMALE             2              60
  MALE               1              73
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SARS2 MUTATED                                     1
  SARS2 WILD-TYPE                                 121
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SARS2 MUTATED                                       2
  SARS2 WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SARS2 MUTATED                                                  0
  SARS2 WILD-TYPE                                                2
D184V8, multiclass
                                                  clus
vv                                                 SARS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SARS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          121
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V9, continuous
[1] "Remove cluster labels:" "SARS2 MUTATED"         
clus
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              46 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A4P5 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-AAPS      TCGA-FB-AAPY 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-H6-8124      TCGA-H6-A45N      TCGA-HZ-A77Q      TCGA-HZ-A8P0 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-US-A774 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-YY-A8LH 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
D184V10, continuous
[1] "Remove cluster labels:" "SARS2 MUTATED"         
clus
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              37 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-HZ-A77Q 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7891 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-YY-A8LH 
"SARS2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SARS2 MUTATED    3  0  0  0
  SARS2 WILD-TYPE 74 48  1  3
D184V11, multiclass
    clus
vv   SARS2 MUTATED SARS2 WILD-TYPE
  R0             3              74
  R1             0              48
  R2             0               1
  RX             0               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SARS2 MUTATED       0                         0     3
  SARS2 WILD-TYPE     2                         5   122
D184V13, multiclass
                           clus
vv                          SARS2 MUTATED SARS2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V14, binary
                 cls
clus                0   1
  SARS2 MUTATED     0   2
  SARS2 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    2
  SARS2 WILD-TYPE    3  102
                        clus
vv                       SARS2 MUTATED SARS2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             102
[1] 2 2
[1] FALSE

Clustering(185) Variable = ADORA3 MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2               0  1
  ADORA3 MUTATED    3  2
  ADORA3 WILD-TYPE 59 70
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              129 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               2               70 
$`ADORA3 MUTATED`
TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-AAUU TCGA-LB-A7SX 
       19.82        21.30        17.16         8.05        12.92 

$`ADORA3 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98         2.47        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.40         9.44        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
        0.39        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  ADORA3 MUTATED ADORA3 WILD-TYPE 
            8.05             0.13 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           21.30            75.12 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           17.16            13.68 
[1] "8.1 - 21.3 (17.2)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.4"
D185V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ADORA3 MUTATED          0        0         0         5         0        0
  ADORA3 WILD-TYPE        4        6        20        94         4        3
D185V3, multiclass
           clus
vv          ADORA3 MUTATED ADORA3 WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              0               20
  STAGE IIB              5               94
  STAGE III              0                4
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ADORA3 MUTATED     0   0     5
  ADORA3 WILD-TYPE   5  13   113
D185V4, multiclass
       clus
vv      ADORA3 MUTATED ADORA3 WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              5              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V5, binary
                  cls
clus                0  1
  ADORA3 MUTATED    0  5
  ADORA3 WILD-TYPE 32 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      0    5
  ADORA3 WILD-TYPE   32   99
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0              0               32
  1              5               99
[1] 2 2
[1] FALSE
D185V6, binary
                  cls
clus                0  1
  ADORA3 MUTATED    4  0
  ADORA3 WILD-TYPE 58  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      4    0
  ADORA3 WILD-TYPE   58    3
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0              4               58
  1              0                3
[1] 2 2
[1] FALSE
D185V7, binary
                  cls
clus                0  1
  ADORA3 MUTATED    3  2
  ADORA3 WILD-TYPE 59 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      3    2
  ADORA3 WILD-TYPE   59   72
        clus
vv       ADORA3 MUTATED ADORA3 WILD-TYPE
  FEMALE              3               59
  MALE                2               72
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ADORA3 MUTATED                                     5
  ADORA3 WILD-TYPE                                 117
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ADORA3 MUTATED                                       0
  ADORA3 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ADORA3 MUTATED                                                  0
  ADORA3 WILD-TYPE                                                2
D185V8, multiclass
                                                  clus
vv                                                 ADORA3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ADORA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V9, continuous
D185V10, continuous
                  vv
clus               R0 R1 R2 RX
  ADORA3 MUTATED    3  2  0  0
  ADORA3 WILD-TYPE 74 46  1  3
D185V11, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  R0              3               74
  R1              2               46
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADORA3 MUTATED       0                         1     4
  ADORA3 WILD-TYPE     2                         4   121
D185V13, multiclass
                           clus
vv                          ADORA3 MUTATED ADORA3 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V14, binary
                  cls
clus                0  1
  ADORA3 MUTATED    0  5
  ADORA3 WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      0    5
  ADORA3 WILD-TYPE    3   99
                        clus
vv                       ADORA3 MUTATED ADORA3 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5               99
[1] 2 2
[1] FALSE

Clustering(186) Variable = ATP11B MUTATION ANALYSIS
D186V1, survival
                  sevent
clus2               0  1
  ATP11B MUTATED    2  2
  ATP11B WILD-TYPE 60 70
  ATP11B MUTATED ATP11B WILD-TYPE 
               4              130 
  ATP11B MUTATED ATP11B WILD-TYPE 
               2               70 
$`ATP11B MUTATED`
TCGA-IB-7651 TCGA-RB-A7B8 TCGA-US-A776 TCGA-YH-A8SY 
       19.82        15.32        27.75        12.76 

$`ATP11B WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
        6.02        11.11         7.40         9.44         8.05        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        3.12         9.40        21.24        17.26        23.08        22.85 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        66.28         0.69 

  ATP11B MUTATED ATP11B WILD-TYPE 
           12.76             0.13 
  ATP11B MUTATED ATP11B WILD-TYPE 
           27.75            75.12 
  ATP11B MUTATED ATP11B WILD-TYPE 
           17.57            13.50 
[1] "12.8 - 27.8 (17.6)" "0.1 - 75.1 (13.5)" 
[1] "hr=" "1.4"
D186V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ATP11B MUTATED          0        0         1         2         1        0
  ATP11B WILD-TYPE        4        6        19        97         3        3
D186V3, multiclass
           clus
vv          ATP11B MUTATED ATP11B WILD-TYPE
  STAGE IA               0                4
  STAGE IB               0                6
  STAGE IIA              1               19
  STAGE IIB              2               97
  STAGE III              1                3
  STAGE IV               0                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP11B MUTATED     0   0     4
  ATP11B WILD-TYPE   5  13   114
D186V4, multiclass
       clus
vv      ATP11B MUTATED ATP11B WILD-TYPE
  T1                 0                5
  T2                 0               13
  T3+T4              4              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V5, binary
                  cls
clus                 0   1
  ATP11B MUTATED     1   3
  ATP11B WILD-TYPE  31 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      1    3
  ATP11B WILD-TYPE   31  101
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0              1               31
  1              3              101
[1] 2 2
[1] FALSE
D186V6, binary
                  cls
clus                0  1
  ATP11B MUTATED    1  0
  ATP11B WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      1    0
  ATP11B WILD-TYPE   61    3
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0              1               61
  1              0                3
[1] 2 2
[1] FALSE
D186V7, binary
                  cls
clus                0  1
  ATP11B MUTATED    3  1
  ATP11B WILD-TYPE 59 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      3    1
  ATP11B WILD-TYPE   59   73
        clus
vv       ATP11B MUTATED ATP11B WILD-TYPE
  FEMALE              3               59
  MALE                1               73
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP11B MUTATED                                     1
  ATP11B WILD-TYPE                                 121
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP11B MUTATED                                       1
  ATP11B WILD-TYPE                                    10
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP11B MUTATED                                                  1
  ATP11B WILD-TYPE                                                1
D186V8, multiclass
                                                  clus
vv                                                 ATP11B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 ATP11B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           121
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V9, continuous
[1] "Remove cluster labels:" "ATP11B MUTATED"        
clus
  ATP11B MUTATED ATP11B WILD-TYPE 
               1               47 
      TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-FB-A4P5       TCGA-FB-A4P6       TCGA-FB-A5VM       TCGA-FB-A78T 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPY       TCGA-H6-8124       TCGA-H6-A45N 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-YY-A8LH 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
D186V10, continuous
[1] "Remove cluster labels:" "ATP11B MUTATED"        
clus
  ATP11B MUTATED ATP11B WILD-TYPE 
               1               38 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-YY-A8LH 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATP11B MUTATED    3  0  0  0
  ATP11B WILD-TYPE 74 48  1  3
D186V11, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  R0              3               74
  R1              0               48
  R2              0                1
  RX              0                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP11B MUTATED       0                         0     4
  ATP11B WILD-TYPE     2                         5   121
D186V13, multiclass
                           clus
vv                          ATP11B MUTATED ATP11B WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V14, binary
                  cls
clus                 0   1
  ATP11B MUTATED     0   4
  ATP11B WILD-TYPE   3 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      0    4
  ATP11B WILD-TYPE    3  100
                        clus
vv                       ATP11B MUTATED ATP11B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              100
[1] 2 2
[1] FALSE

Clustering(187) Variable = RAG1 MUTATION ANALYSIS
D187V1, survival
                sevent
clus2             0  1
  RAG1 MUTATED    2  1
  RAG1 WILD-TYPE 60 71
  RAG1 MUTATED RAG1 WILD-TYPE 
             3            131 
  RAG1 MUTATED RAG1 WILD-TYPE 
             1             71 
$`RAG1 MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABO TCGA-IB-7651 
        2.63        14.47        19.82 

$`RAG1 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV 
       22.72        22.26        15.91        14.40         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
        4.70        22.49         3.39        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       23.61        20.84         7.36        24.26        28.73        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
        7.66        19.27         3.12        17.00         5.88        11.93 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        12.43         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       23.54        15.55         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       13.84        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       17.92        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        21.90        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         9.44         8.05        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  RAG1 MUTATED RAG1 WILD-TYPE 
          2.63           0.13 
  RAG1 MUTATED RAG1 WILD-TYPE 
         19.82          75.12 
  RAG1 MUTATED RAG1 WILD-TYPE 
         14.47          13.68 
[1] "2.6 - 19.8 (14.5)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D187V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RAG1 MUTATED          0        0         0         3         0        0
  RAG1 WILD-TYPE        4        6        20        96         4        3
D187V3, multiclass
           clus
vv          RAG1 MUTATED RAG1 WILD-TYPE
  STAGE IA             0              4
  STAGE IB             0              6
  STAGE IIA            0             20
  STAGE IIB            3             96
  STAGE III            0              4
  STAGE IV             0              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  RAG1 MUTATED     0   0     3
  RAG1 WILD-TYPE   5  13   115
D187V4, multiclass
       clus
vv      RAG1 MUTATED RAG1 WILD-TYPE
  T1               0              5
  T2               0             13
  T3+T4            3            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V5, binary
                cls
clus               0   1
  RAG1 MUTATED     0   3
  RAG1 WILD-TYPE  32 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      0    3
  RAG1 WILD-TYPE   32  101
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0            0             32
  1            3            101
[1] 2 2
[1] FALSE
D187V6, binary
                cls
clus              0  1
  RAG1 MUTATED    3  0
  RAG1 WILD-TYPE 59  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      3    0
  RAG1 WILD-TYPE   59    3
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0            3             59
  1            0              3
[1] 2 2
[1] FALSE
D187V7, binary
                cls
clus              0  1
  RAG1 MUTATED    1  2
  RAG1 WILD-TYPE 61 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      1    2
  RAG1 WILD-TYPE   61   72
        clus
vv       RAG1 MUTATED RAG1 WILD-TYPE
  FEMALE            1             61
  MALE              2             72
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAG1 MUTATED                                     3
  RAG1 WILD-TYPE                                 119
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAG1 MUTATED                                       0
  RAG1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAG1 MUTATED                                                  0
  RAG1 WILD-TYPE                                                2
D187V8, multiclass
                                                  clus
vv                                                 RAG1 MUTATED RAG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V9, continuous
[1] "Remove cluster labels:" "RAG1 MUTATED"          
clus
  RAG1 MUTATED RAG1 WILD-TYPE 
             2             46 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A4P5 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N     TCGA-HZ-A77Q 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7891 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-US-A774 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-YY-A8LH 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
D187V10, continuous
[1] "Remove cluster labels:" "RAG1 MUTATED"          
clus
  RAG1 MUTATED RAG1 WILD-TYPE 
             2             37 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-3A-A9IB 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" "RAG1 WILD-TYPE" 
    TCGA-YY-A8LH 
"RAG1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RAG1 MUTATED    2  1  0  0
  RAG1 WILD-TYPE 75 47  1  3
D187V11, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  R0            2             75
  R1            1             47
  R2            0              1
  RX            0              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAG1 MUTATED       0                         0     3
  RAG1 WILD-TYPE     2                         5   122
D187V13, multiclass
                           clus
vv                          RAG1 MUTATED RAG1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V14, binary
                cls
clus               0   1
  RAG1 MUTATED     0   1
  RAG1 WILD-TYPE   3 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      0    1
  RAG1 WILD-TYPE    3  103
                        clus
vv                       RAG1 MUTATED RAG1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            1            103
[1] 2 2
[1] FALSE

Clustering(188) Variable = HK2 MUTATION ANALYSIS
D188V1, survival
               sevent
clus2            0  1
  HK2 MUTATED    2  2
  HK2 WILD-TYPE 60 70
  HK2 MUTATED HK2 WILD-TYPE 
            4           130 
  HK2 MUTATED HK2 WILD-TYPE 
            2            70 
$`HK2 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-AAUU 
       19.82        41.33         3.62         8.05 

$`HK2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        14.47        14.40 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       28.73        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
        5.88        11.93        24.07        14.76        12.43         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        1.02        12.89        13.84        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93        17.92        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        4.04        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.40         9.44        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       14.14         0.39        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  HK2 MUTATED HK2 WILD-TYPE 
         3.62          0.13 
  HK2 MUTATED HK2 WILD-TYPE 
        41.33         75.12 
  HK2 MUTATED HK2 WILD-TYPE 
       13.935        13.745 
[1] "3.6 - 41.3 (13.9)" "0.1 - 75.1 (13.7)"
[1] "hr=" "1.2"
D188V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HK2 MUTATED          0        0         0         4         0        0
  HK2 WILD-TYPE        4        6        20        95         4        3
D188V3, multiclass
           clus
vv          HK2 MUTATED HK2 WILD-TYPE
  STAGE IA            0             4
  STAGE IB            0             6
  STAGE IIA           0            20
  STAGE IIB           4            95
  STAGE III           0             4
  STAGE IV            0             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  HK2 MUTATED     0   0     4
  HK2 WILD-TYPE   5  13   114
D188V4, multiclass
       clus
vv      HK2 MUTATED HK2 WILD-TYPE
  T1              0             5
  T2              0            13
  T3+T4           4           114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V5, binary
               cls
clus              0   1
  HK2 MUTATED     0   4
  HK2 WILD-TYPE  32 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK2 MUTATED      0    4
  HK2 WILD-TYPE   32  100
   clus
vv  HK2 MUTATED HK2 WILD-TYPE
  0           0            32
  1           4           100
[1] 2 2
[1] FALSE
D188V6, binary
               cls
clus             0  1
  HK2 MUTATED    4  0
  HK2 WILD-TYPE 58  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK2 MUTATED      4    0
  HK2 WILD-TYPE   58    3
   clus
vv  HK2 MUTATED HK2 WILD-TYPE
  0           4            58
  1           0             3
[1] 2 2
[1] FALSE
D188V7, binary
               cls
clus             0  1
  HK2 MUTATED    3  1
  HK2 WILD-TYPE 59 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK2 MUTATED      3    1
  HK2 WILD-TYPE   59   73
        clus
vv       HK2 MUTATED HK2 WILD-TYPE
  FEMALE           3            59
  MALE             1            73
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HK2 MUTATED                                     4
  HK2 WILD-TYPE                                 118
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HK2 MUTATED                                       0
  HK2 WILD-TYPE                                    11
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HK2 MUTATED                                                  0
  HK2 WILD-TYPE                                                2
D188V8, multiclass
                                                  clus
vv                                                 HK2 MUTATED HK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V9, continuous
D188V10, continuous
[1] "Remove cluster labels:" "HK2 MUTATED"           
clus
  HK2 MUTATED HK2 WILD-TYPE 
            2            37 
   TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO    TCGA-3A-A9IB 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-FB-A4P5    TCGA-FB-A4P6    TCGA-FB-A5VM    TCGA-FB-A78T 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-FB-AAPY    TCGA-H6-8124    TCGA-HZ-A77Q    TCGA-HZ-A8P0 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649    TCGA-IB-7886    TCGA-IB-7891 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-LB-A7SX 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-US-A774    TCGA-XD-AAUI 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" "HK2 WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-YY-A8LH 
"HK2 WILD-TYPE" "HK2 WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  HK2 MUTATED    3  1  0  0
  HK2 WILD-TYPE 74 47  1  3
D188V11, multiclass
    clus
vv   HK2 MUTATED HK2 WILD-TYPE
  R0           3            74
  R1           1            47
  R2           0             1
  RX           0             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HK2 MUTATED       0                         0     4
  HK2 WILD-TYPE     2                         5   121
D188V13, multiclass
                           clus
vv                          HK2 MUTATED HK2 WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V14, binary
               cls
clus              0   1
  HK2 MUTATED     0   4
  HK2 WILD-TYPE   3 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK2 MUTATED      0    4
  HK2 WILD-TYPE    3  100
                        clus
vv                       HK2 MUTATED HK2 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4           100
[1] 2 2
[1] FALSE
